| 2000 | 1 | 1 | Adrian Gonzalez | 1B | Eastlake High School (Chula Vista, CA) | Florida | |
| 2000 | 1 | 2 | Adam Johnson | P | Cal State Fullerton | Minnesota | |
| 2000 | 1 | 3 | Luis Montanez | IF | Coral Park (Miami, FL) | Chi. Cubs | |
| 2000 | 1 | 4 | Mike Stodolka | P | Centennial High School (Corona, CA) | Kansas City | |
| 2000 | 1 | 5 | Justin Wayne | P | Stanford University | Montreal | |
| 2000 | 1 | 6 | Rocco Baldelli | OF | Bishop Hendricken High School (Warwick, RI) | Tampa Bay | |
| 2000 | 1 | 7 | Matt Harrington | P | Palmdale (Palmdale, CA) | Colorado | |
| 2000 | 1 | 8 | Matthew Wheatland | Pæ | Rancho Bernardo (San Diego, CA) | Detroit | |
| 2000 | 1 | 9 | Mark Phillips | P | Hanover (Hanover,PA) | San Diego | |
| 2000 | 1 | 10 | Joe Torres | P | Gateway (Kissimmee,FL) | Anaheim | |
| 2000 | 1 | 11 | Dave Kryznel | OF | Green Valley High School (Henderson, NV) | Milwaukee | |
| 2000 | 1 | 12 | Joe Borchard | OF | Stanford University | Chi. White Sox | |
| 2000 | 1 | 13 | Shaun Boyd | IF | Vista (Vista, CA) | StL Cardinals | |
| 2000 | 1 | 14 | Beau Hale | P | University of Texas | Baltimore | |
| 2000 | 1 | 15 | Chase Utley | IF | UCLA | Philadelphia | |
| 2000 | 1 | 16 | Billy Traber | P | Loyola Marymount University | NY Mets | |
| 2000 | 1 | 17 | Ben Diggins | P | University of Arizona | LA Dodgers | |
| 2000 | 1 | 18 | Miguel Negron | OF | - | Toronto | |
| 2000 | 1 | 19 | Sean Burnett | P | Wellington Christian (Wellington,FL) | Pittsburgh | |
| 2000 | 1 | 20 | Chris Bootcheck | P | Auburn University | Anaheim | |
| 2000 | 1 | 21 | Boof Bonser | P | Gibbs (St. Petersburg,FL) | San Francisco | |
| 2000 | 1 | 22 | Phil Dumatrait | P | Bakersfield College | Boston | |
| 2000 | 1 | 23 | David Espinosa | SS | Gulliver Prep (Coral Gables,FL) | Cincinnati | |
| 2000 | 1 | 24 | Blake Williams | P | Texas State University | StL Cardinals | |
| 2000 | 1 | 25 | Scott Heard | C | Rancho Bernardo (San Diego, CA) | Texas | |
| 2000 | 1 | 26 | Corey Smith | IF | Piscataway (Piscataway,NJ) | Cleveland | |
| 2000 | 1 | 27 | Robert Stiehl | Cæ | El Camino College | Houston | |
| 2000 | 1 | 28 | David Parrish | C | University of Michigan | NY Yankees | |
| 2000 | 1 | 29 | Adam Wainwright | P | Glynn Academy (Brunswick,GA) | Atlanta | |
| 2000 | 1 | 30 | Scott Thorman | IF | Preston (Cambridge,ON) | Atlanta | |
| 2000 | 1 | 31 | Aaron Heilman | P | University of Notre Dame | Minnesota | |
| 2000 | 1 | 32 | Tripper Johnson | 3B | Newport High School (Bellevue, WA) | Baltimore | |
| 2000 | 1 | 33 | Dustin McGowan | P | Long County High School (Ludowici, GA) | Toronto | |
| 2000 | 1 | 34 | Dustin Moseley | P | Arkansas (Texarkana,AR) | Cincinnati | |
| 2000 | 1 | 35 | Tyrell Godwin | CF | University of North Carolina | Texas | |
| 2000 | 1 | 36 | Bob Keppel | P | De Smet Jesuit (Creve Coeur,MO) | NY Mets | |
| 2000 | 1 | 37 | Derek Thompson | P | Land O'Lakes High School (Land O'Lakes, FL) | Cleveland | |
| 2000 | 1 | 38 | Kelly Johnson | P | Westwood High School (Austin, TX) | Atlanta | |
| 2000 | 1 | 39 | Chad Hawkins | P | Baylor University | Texas | |
| 2000 | 1 | 40 | Aaron Herr | IF | Hempfield (Landisville,PA) | Atlanta | |
| 2000 | 2 | 41 | Jason Stokes | IF | Coppell High School (Coppell,TX) | Florida | |
| 2000 | 2 | 42 | Tagg Bozied | 1B | University of San Francisco | Minnesota | |
| 2000 | 2 | 43 | Bobby Hill | 2B | University of Miami | Chi. Cubs | |
| 2000 | 2 | 44 | Michael Tonis | C | University of California | Kansas City | |
| 2000 | 2 | 45 | Peter Bauer | P | University of South Carolina | Toronto | |
| 2000 | 2 | 46 | Dane Sardinha | C | Pepperdone University | Cincinnati | |
| 2000 | 2 | 47 | Jason Young | P | Stanford University | Colorado | |
| 2000 | 2 | 48 | Chad Petty | P | Chalker (Southington,OH) | Detroit | |
| 2000 | 2 | 49 | Xavier Nady | OF | University of California | San Diego | |
| 2000 | 2 | 50 | Jared Abruzzo | C | El Capitan High School (Lakeside, CA) | Anaheim | |
| 2000 | 2 | 51 | Bubba Nelson | P | Riverdale Baptist (Upper Marlboro,MD) | Atlanta | |
| 2000 | 2 | 52 | Tim Hummel | 2B | Old Dominion University | Chi. White Sox | |
| 2000 | 2 | 53 | Chris Narveson | P | Roberson High School (Asheville, NC) | StL Cardinals | |
| 2000 | 2 | 54 | J.D. Durbin | P | Coronado (Scottsdale, AZ) | Minnesota | |
| 2000 | 2 | 55 | Brian Tallet | P | Louisiana State University | Cleveland | |
| 2000 | 2 | 56 | Jay Bourgeois | IF | Forest Brook High School (Houston, TX) | Texas | |
| 2000 | 2 | 57 | Joel Hanrahan | P | Norwalk Community (Norwalk,IA) | LA Dodgers | |
| 2000 | 2 | 58 | Dominic Rich | IF | Auburn University | Toronto | |
| 2000 | 2 | 59 | David Beigh | P | Harrison High School (West Lafayette,IN) | Pittsburgh | |
| 2000 | 2 | 60 | Freddie Bynum | IF | Pitt Community College | Oakland | |
| 2000 | 2 | 61 | Lance Niekro | IF | Florida Southern College | San Francisco | |
| 2000 | 2 | 62 | Manny Delcarmen | P | West Roxbury (West Roxbury,MA) | Boston | |
| 2000 | 2 | 63 | Ryan Snare | P | University of North Carolina | Cincinnati | |
| 2000 | 2 | 64 | Randy Truselo | P | Delcastle (Wilmington,DE) | Texas | |
| 2000 | 2 | 65 | Matthew Peterson | P | Rapides School (Lecompte,LA) | NY Mets | |
| 2000 | 2 | 66 | Kenneth Folsom | RF | West Orange High School (Winter Garden, FL) | Cleveland | |
| 2000 | 2 | 67 | Chad Qualls | P | University of Nevada | Houston | |
| 2000 | 2 | 68 | Danny Borrell | P | Wake Forest University | NY Yankees | |
| 2000 | 2 | 69 | Michael Schultz | P | Loyola Marymount University | Arizona | |
| 2000 | 2 | 70 | Bryan Digby | P | McIntosh High School (Peachtree City, GA) | Atlanta | |
| 2000 | 3 | 75 | Grady Sizemore | OF | Cascade High School (Everett, WA) | Montreal | |
| 2000 | 3 | 78 | Exavier Logan | SS | Copiah-Lincoln Community College | Detroit | |
| 2000 | 3 | 80 | Tom Murphy | P | Florida Atlantic University | Anaheim | |
| 2000 | 3 | 82 | Mike Morse | IF | Nova (Davie,FL) | Chi. White Sox | |
| 2000 | 3 | 89 | Christopher Young | P | Princeton University | Pittsburgh | |
| 2000 | 3 | 99 | Bill White | P | Jacksonville State University | Arizona | |
| 2000 | 3 | 100 | Blaine Boyer | P | Walton High School (Marietta, GA) | Atlanta | |
| 2000 | 4 | 102 | Jason Miller | P | Sarasota High School (Sarasota, FL) | Minnesota | |
| 2000 | 4 | 103 | Todd Wellemeyer | P | Bellarmine University | Chi. Cubs | |
| 2000 | 4 | 104 | David DeJesus | OF | Rutgers University | Kansas City | |
| 2000 | 4 | 105 | Cliff Lee | P | University of Arkansas | Montreal | |
| 2000 | 4 | 106 | Zach Miner | P | Palm Beach Gardens (Palm Beach Gardens,FL) | Atlanta | |
| 2000 | 4 | 107 | Cory Vance | P | Georgia Institute of Technology | Colorado | |
| 2000 | 4 | 108 | Mark Woodyard | P | Bethune-Cookman University | Detroit | |
| 2000 | 4 | 113 | Yadier Molina | C | Maestro Ladi (Vega Alta,PR) | StL Cardinals | |
| 2000 | 4 | 117 | Koyie Hill | C | Wichita State University | LA Dodgers | |
| 2000 | 4 | 124 | Laynce Nix | OF | Midland High School (Midland, TX) | Texas | |
| 2000 | 4 | 128 | Matt Smith | LHP | Oklahoma State University | NY Yankees | |
| 2000 | 4 | 129 | Josh Kroeger | OF | Scripps Ranch (San Diego, CA) | Arizona | |
| 2000 | 5 | 134 | Zach McClellan | P | Indiana University | Kansas City | |
| 2000 | 5 | 137 | Garrett Atkins | IF | University of California-Irvine | Colorado | |
| 2000 | 5 | 139 | Jon Huber | P | North Fort Myers (Fort Myers, FL) | San Diego | |
| 2000 | 5 | 140 | Bobby Jenks | P | Inglemoor (Spirit Lake,ID) | Anaheim | |
| 2000 | 5 | 148 | Mike Smith | P | University of Richmond | Toronto | |
| 2000 | 5 | 152 | Brian Esposito | C-1B | University of Connecticut | Boston | |
| 2000 | 5 | 160 | Chris Waters | P | South Florida Community College | Atlanta | |
| 2000 | 6 | 164 | Brian Bass | P | Robert E. Lee (Montgomery,AL) | Kansas City | |
| 2000 | 6 | 165 | Shawn Hill | P | Bishop P.F. Reding Catholic (Georgetown,ON) | Montreal | |
| 2000 | 6 | 167 | Scott Dohmann | P | University of Louisiana at Lafayette | Colorado | |
| 2000 | 6 | 175 | Taylor Buchholz | P | Springfield (Springfield,PA) | Philadelphia | |
| 2000 | 6 | 176 | Jamal Strong | OF | University of Nebraska | Seattle | |
| 2000 | 6 | 178 | Richard Thompson | H | James Madison University | Toronto | |
| 2000 | 6 | 185 | Chris Basak | SS | University of Illinois | NY Mets | |
| 2000 | 7 | 193 | Ryan Jorgensen | C | Louisiana State University | Chi. Cubs | |
| 2000 | 7 | 195 | Wes Littleton | P | Vista (Vista, CA) | Montreal | |
| 2000 | 7 | 200 | Aaron Hill | SS | Redwood High School (Visalia, CA) | Anaheim | |
| 2000 | 7 | 206 | Jaime Bubela | OF | Baylor University | Seattle | |
| 2000 | 7 | 210 | Marc Gwyn | P | Rice University | Oakland | |
| 2000 | 7 | 211 | Erick Threets | P | Modesto Junior College | San Francisco | |
| 2000 | 7 | 214 | Virgil Vasquez | P | Santa Barbara High School (Santa Barbara, CA) | Texas | |
| 2000 | 7 | 215 | Jeff Duncan | OF | Arizona State University | NY Mets | |
| 2000 | 7 | 218 | Mitch Jones | IF | Arizona State University | NY Yankees | |
| 2000 | 7 | 219 | Tim Olson | SS | University of Florida | Arizona | |
| 2000 | 8 | 223 | Dontrelle Willis | P | Encinal (Alameda,cA) | Chi. Cubs | |
| 2000 | 8 | 225 | Phil Seibel | P | University of Texas | Montreal | |
| 2000 | 8 | 226 | Mark Malaska | P | University of Akron | Tampa Bay | |
| 2000 | 8 | 244 | Nicholas Masset | P | Pinellas Park (Pinellas Park,FL) | Texas | |
| 2000 | 8 | 246 | Joe Inglett | IF | University of Nevada | Cleveland | |
| 2000 | 8 | 247 | Cory Doyne | P | Land O'Lakes High School (Land O'Lakes, FL) | Houston | |
| 2000 | 8 | 249 | Brandon Webb | P | University of Kentucky | Arizona | |
| 2000 | 9 | 266 | Charlie Manning | P | University of Tampa | Seattle | |
| 2000 | 9 | 267 | Humberto Sanchez | P | South Bronx (Bronx, NY) | LA Dodgers | |
| 2000 | 9 | 270 | Marshall McDougall | IF | Florida State University | Oakland | |
| 2000 | 9 | 274 | Edwin Encarnacion | IF | - | Texas | |
| 2000 | 9 | 277 | Eric Bruntlett | IF | Stanford University | Houston | |
| 2000 | 10 | 287 | Clint Barmes | IF | Indiana State University | Colorado | |
| 2000 | 10 | 290 | Matt Hensley | P | Grossmont College | Anaheim | |
| 2000 | 10 | 292 | Heath Phillips | P | Evansville Central (Evansville,IN) | Chi. White Sox | |
| 2000 | 10 | 293 | Carmen Cali | P | Florida Atlantic University | StL Cardinals | |
| 2000 | 10 | 301 | Adam Shabala | OF | University of Nebraska | San Francisco | |
| 2000 | 10 | 308 | Jason Anderson | P | University of Illinois | NY Yankees | |
| 2000 | 11 | 312 | Josh Rabe | OF | Quincy University | Minnesota | |
| 2000 | 11 | 313 | Jon Leicester | P | University of Memphis | Chi. Cubs | |
| 2000 | 11 | 314 | Ryan Bukvich | P | University of Mississippi | Kansas City | |
| 2000 | 11 | 317 | Brad Hawpe | IF | Louisiana State University | Colorado | |
| 2000 | 11 | 321 | Corey Hart | LF | Greenwood (Bowling Green,KY) | Milwaukee | |
| 2000 | 11 | 323 | John Gall | 1B | Stanford University | StL Cardinals | |
| 2000 | 11 | 327 | Joseph Nance | P | University of Houston | LA Dodgers | |
| 2000 | 11 | 332 | Freddy Sanchez | 2B | Oklahoma City University | Boston | |
| 2000 | 11 | 337 | Bob McCrory | P | Columbus High School (Columbus, MS) | Houston | |
| 2000 | 12 | 342 | Jason Kubel | OF | Highland (Palmdale, CA) | Minnesota | |
| 2000 | 12 | 347 | Sean Green | P | University of Louisville | Colorado | |
| 2000 | 12 | 358 | Vinnie Chulk | P | Saint Thomas University | Toronto | |
| 2000 | 12 | 369 | Brian Bruney | P | Warrenton (Warrenton,OR) | Arizona | |
| 2000 | 13 | 379 | Justin Germano | P | Claremont High School (Claremont, CA) | San Diego | |
| 2000 | 13 | 385 | Carlos Rivera | 1B | - | Philadelphia | |
| 2000 | 13 | 391 | Justin Knoedler | P | Lincoln Land Community College | San Francisco | |
| 2000 | 14 | 403 | Jason Dubois | OF | Virginia Commonwealth University | Chi. Cubs | |
| 2000 | 14 | 426 | Ryan Church | OF | University of Nevada | Cleveland | |
| 2000 | 15 | 434 | Adam Peterson | P | Wichita State University | Kansas City | |
| 2000 | 15 | 437 | Justin Huisman | P | University of Mississippi | Colorado | |
| 2000 | 15 | 450 | Kevin Barry | P | Rider University | Oakland | |
| 2000 | 15 | 457 | Todd Self | OF | University of Louisiana at Lafayette | Houston | |
| 2000 | 16 | 466 | James Shields | P | William S. Hart High School (Newhall, CA) | Tampa Bay | |
| 2000 | 17 | 491 | Josh Willingham | 2B | University of North Alabama | Florida | |
| 2000 | 17 | 492 | Paul Maholm | P | Germantown High School (Germantown, TN) | Minnesota | |
| 2000 | 17 | 500 | Mike Napoli | C | Flanagan High School (Pembroke Pines, FL) | Anaheim | |
| 2000 | 17 | 505 | Travis Chapman | IF | Mississippi State University | Philadelphia | |
| 2000 | 17 | 510 | Rich Harden | P | Central Arizona College | Oakland | |
| 2000 | 17 | 519 | Doug Slaten | P | Los Angeles Pierce College | Arizona | |
| 2000 | 17 | 520 | Trey Hodges | P | Louisiana State University | Atlanta | |
| 2000 | 18 | 523 | Buck Coats | OF | Valdosta High School (Valdosta, GA) | Chi. Cubs | |
| 2000 | 19 | 574 | Arlington Murray | P | Uintah (Vernal,UT) | Texas | |
| 2000 | 19 | 577 | Michael Bourn | OF | Nimitz (Houston, TX) | Houston | |
| 2000 | 19 | 578 | Brad Halsey | P | Hill College | NY Yankees | |
| 2000 | 19 | 580 | Charles Thomas | OF | Western Carolina University | Atlanta | |
| 2000 | 20 | 583 | Carmen Pignatiello | P | Providence College | Chi. Cubs | |
| 2000 | 20 | 585 | Fred Lewis | OF | Mississippi Gulf Coast Community College | Montreal | |
| 2000 | 20 | 599 | Jose Bautista | 3B | Chipola College | Pittsburgh | |
| 2000 | 22 | 645 | Jason Bay | OF | Gonzaga University | Montreal | |
| 2000 | 22 | 649 | J.J. Furmaniak | IF | Lewis University | San Diego | |
| 2000 | 22 | 661 | Jason Ellison | OF | Lewis-Clark State College | San Francisco | |
| 2000 | 23 | 686 | Jason Hammel | P | South Kitsap (Port Orchard,WA) | Seattle | |
| 2000 | 23 | 693 | Steve Smitherman | OF | University of Arkansas-Little Rock | Cincinnati | |
| 2000 | 24 | 704 | Mike Matthews | P | Columbia State Community College | Kansas City | |
| 2000 | 24 | 706 | Shawn Riggans | C | Indian River State College | Tampa Bay | |
| 2000 | 24 | 729 | Andrew Green | University of Kentucky | Arizona | ||
| 2000 | 25 | 739 | Joe Cassel | P | Los Angeles Pierce College | San Diego | |
| 2000 | 25 | 749 | Nate McLouth | OF | Whitehall (Whitehall,MI) | Pittsburgh | |
| 2000 | 26 | 769 | Chad Cordero | P | Don Antonio Lugo (Chino, CA) | San Diego | |
| 2000 | 26 | 779 | Ian Snell | P | Caesar Rodney (Camden,DE) | Pittsburgh | |
| 2000 | 26 | 788 | Sean Henn | P | McLennan Community College | NY Yankees | |
| 2000 | 27 | 793 | Jason Szuminski | P | Massachusetts Institute of Technology | Chi. Cubs | |
| 2000 | 27 | 799 | Kevin Reese | OF | University of San Diego | San Diego | |
| 2000 | 28 | 822 | Daniel Davidson | P | Gulf Coast Community College | Minnesota | |
| 2000 | 28 | 841 | Alex Hinshaw | P | Claremont High School (Claremont, CA) | San Francisco | |
| 2000 | 29 | 867 | Ryan Sadowski | P | Western (Davie,FL) | LA Dodgers | |
| 2000 | 29 | 870 | Ron Flores | P | University of Southern California | Oakland | |
| 2000 | 29 | 872 | Kason Gabbard | P | Royal Palm Beach (West Palm Beach, FL) | Boston | |
| 2000 | 29 | 876 | Jonathan Van Every | OF | Itawamba Community College | Cleveland | |
| 2000 | 29 | 879 | Ian Kinsler | SS | Canyon del Oro (Tucson, AZ) | Arizona | |
| 2000 | 29 | 880 | Adam LaRoche | 1B | Seminole State College | Atlanta | |
| 2000 | 30 | 886 | Edgar Gonzalez | IF | University of San Diego | Tampa Bay | |
| 2000 | 30 | 896 | Chip Ambres | OF | Ranger College | Seattle | |
| 2000 | 30 | 906 | Brian Wilson | P | Londonderry (Londonderry,NH) | Cleveland | |
| 2000 | 30 | 907 | Mike Burns | P | Cal State Los Angeles | Houston | |
| 2000 | 31 | 914 | Ruben Gotay | IF | Indian Hills Community College-Centerville | Kansas City | |
| 2000 | 31 | 931 | Brian Burres | P | Mount Hood Community College | San Francisco | |
| 2000 | 31 | 936 | Conor Jackson | 1B | El Camino Real (Woodland Hills,CA) | Cleveland | |
| 2000 | 31 | 940 | Delwyn Young | 2B | Littlerock (Lancaster, CA) | Atlanta | |
| 2000 | 32 | 954 | Brandon Fahey | SS-3B | Grayson County College | Baltimore | |
| 2000 | 32 | 968 | Chris Dickerson | OF | Notre Dame High School (Sherman Oaks, CA) | NY Yankees | |
| 2000 | 32 | 970 | Callix Crabbe | 2B | Stone Mountain (Lithonia,GA) | Atlanta | |
| 2000 | 33 | 973 | Larry Barnes | 1B | Pine Bluff High School (Pine Bluff,AR) | Chi. Cubs | |
| 2000 | 33 | 981 | Jon Coutlangus | OF | Indian River State College | Milwaukee | |
| 2000 | 33 | 984 | Kurt BIrkins | RF | Los Angeles Pierce College | Baltimore | |
| 2000 | 33 | 991 | James Lunsford | C | Texas Tech University | San Francisco | |
| 2000 | 33 | 1000 | Anthony Gwynn | OF | Poway High School (Poway, CA) | Atlanta | |
| 2000 | 34 | 1006 | Robert Blackburn | P | Del City (Oklahoma City, OK) | Tampa Bay | |
| 2000 | 34 | 1013 | Tyler Johnson | P | Moorpark College | StL Cardinals | |
| 2000 | 34 | 1014 | Joshua Banks | Severna Park (Severna Park,MD) | Baltimore | ||
| 2000 | 34 | 1021 | Jonathan Albaladejo | P | Colegio Janil (Vega Alta,PR) | San Francisco | |
| 2000 | 35 | 1035 | Russell Jeanson-Martin | 3B | Edouard Montpetit (Montreal,QC) | Montreal | |
| 2000 | 35 | 1037 | Darren Clarke | P | South Florida Community College | Colorado | |
| 2000 | 35 | 1044 | Jeff Salazar | OF | Connors State College | Baltimore | |
| 2000 | 35 | 1052 | Dusty Brown | OF | Bradshaw Mountain (Prescott Valley,AZ) | Boston | |
| 2000 | 36 | 1066 | Kristopher Morton | C | Kings Academy (West Palm Beach, FL) | Tampa Bay | |
| 2000 | 36 | 1074 | Tim Stauffer | P | Central Catholic (Saratoga Springs,NY) | Baltimore | |
| 2000 | 37 | 1096 | Shane Costa | OF | Golden West (Visalia, CA) | Tampa Bay | |
| 2000 | 37 | 1107 | Victor Diaz | IF | Clemente (Chicago, IL) | LA Dodgers | |
| 2000 | 38 | 1126 | Steven Jackson | P | Summerville (Summerville,SC) | Tampa Bay | |
| 2000 | 38 | 1132 | Tom Gorzelanny | P | Marist (Chicago, IL) | Chi. White Sox | |
| 2000 | 38 | 1137 | Brian Barton | LF | Westchester High School (Los Angeles, CA) | LA Dodgers | |
| 2000 | 39 | 1158 | Luis Alicea | 2B | Osceola High School (Kissimmee,FL) | Detroit | |
| 2000 | 39 | 1166 | John Nelson | IF | University of Kansas | Seattle | |
| 2000 | 41 | 1234 | Eric Crozier | IF | Norfolk State University | Cleveland | |
| 2000 | 42 | 1262 | Greg Burke | Gloucester Catholic (Gloucester,NJ) | NY Mets | ||
| 2000 | 43 | 1276 | David Sanders | P | Jenks (Jenks,OK) | San Diego | |
| 2000 | 43 | 1287 | Chris Duffy | OF | South Mountain Community College | Boston | |
| 2000 | 43 | 1292 | Jason Windsor | P | Leigh (San Jose, CA) | Houston | |
| 2000 | 44 | 1300 | Anthony Ferrari | P | Lewis-Clark State College | Montreal | |
| 2000 | 44 | 1301 | James Hoffpauir | RF | Lon Morris College | Tampa Bay | |
| 2000 | 45 | 1326 | Jeff Karstens | P | Mount Miguel High School (Spring Valley, CA) | Montreal | |
| 2000 | 45 | 1327 | Luke Scott | OF | Oklahoma State University | Tampa Bay | |
| 2000 | 46 | 1365 | Chris Schroder | P | Oklahoma City University | Cincinnati | |
| 2000 | 48 | 1404 | Cody Clark | C | Fayetteville (Fayetteville,AR) | Toronto | |
| 2000 | 50 | 1439 | David Murphy | OF | Klein High School (Klein, TX) | Anaheim | |
| 2000 | 50 | 1451 | Brian Buscher | 3B | Central Florida Community College | Arizona | |
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