1999 Major League Baseball draft
The 1999 First-Year Player Draft, Major League Baseball's annual amateur draft of high school and college baseball players, was held on June 2 and 3, 1999. A total of 1474 players were drafted over the course of 50 rounds.
First round selections
| Pick | Player | Team | Position | School |
| 1 | Josh Hamilton | Tampa Bay Devil Rays | OF | Athens Drive HS |
| 2 | Josh Beckett | Florida Marlins | P | Spring HS |
| 3 | Glen Duncan | Detroit Tigers | C | University of Southern California |
| 4 | Corey Myers | Arizona Diamondbacks | SS | Desert Vista HS |
| 5 | B.J. Garbe | Minnesota Twins | OF, P | Moses Lake HS |
| 6 | Josh Girdley | Montreal Expos | P | Jasper HS |
| 7 | Kyle Snyder | Kansas City Royals | P | University of North Carolina |
| 8 | Bobby Bradley | Pittsburgh Pirates | P | Wellington Community HS |
| 9 | Barry Zito | Oakland Athletics | P | University of Southern California |
| 10 | Ben Sheets | Milwaukee Brewers | P | Northeast Louisiana University |
| 11 | Ryan Christianson | Seattle Mariners | C | Arlington HS |
| 12 | Brett Myers | Philadelphia Phillies | P | Englewood Senior HS |
| 13 | Mike Paradis | Baltimore Orioles | P | Clemson University |
| 14 | Ty Howington | Cincinnati Reds | P | Hudson's Bay HS |
| 15 | Jason Stumm | Chicago White Sox | P | Centralia HS |
| 16 | Jason Jennings | Colorado Rockies | P | Baylor University |
| 17 | Rick Asadoorian | Boston Red Sox | OF | Northbridge HS |
| 18 | Richard Stahl | Baltimore Orioles | P | Newton County HS |
| 19 | Alex Ríos | Toronto Blue Jays | OF | San Pedro Martin HS |
| 20 | Vince Faison | San Diego Padres | OF | Toombs County HS |
| 21 | Larry Bigbie | Baltimore Orioles | OF | Ball State University |
| 22 | Matt Ginter | Chicago White Sox | P | Mississippi State University |
| 23 | Keith Reed | Baltimore Orioles | OF | Providence College |
| 24 | Kurt Ainsworth | San Francisco Giants | P | Louisiana State University |
| 25 | Mike MacDougal | Kansas City Royals | P | Wake Forest University |
| 26 | Ben Christensen | Chicago Cubs | P | Wichita State University |
| 27 | David Walling | New York Yankees | P | University of Arkansas |
| 28 | Gerik Baxter | San Diego Padres | P | Edmonds Woodway HS |
| 29 | Omar Ortíz | San Diego Padres | P | University of Texas-Pan American |
| 30 | Chance Caple | St. Louis Cardinals | P | Texas A&M University |
Supplemental first round selections
| Pick | Player | Team | Position | School |
| 31 | Casey Daigle | Arizona Diamondbacks | P | Sulphur HS |
| 32 | Jay Gehrke | Kansas City Royals | P | Pepperdine University |
| 33 | Jeff Heaverlo | Seattle Mariners | P | University of Washington |
| 34 | Joshua Cenate | Baltimore Orioles | P | Jefferson HS |
| 35 | Brian West | Chicago White Sox | P | West Monroe HS |
| 36 | Nick Stocks | St. Louis Cardinals | P | Florida State University |
| 37 | Jason Repko | Los Angeles Dodgers | OF | Hanford HS |
| 38 | Colby Lewis | Texas Rangers | P | Bakersfield College |
| 39 | Jerome Williams | San Francisco Giants | P | Waipahu HS |
| 40 | Brad Baker | Boston Red Sox | P | Pioneer Valley Regional HS |
| 41 | Casey Burns | San Diego Padres | P | University of Richmond |
| 42 | Mike Rosamond | Houston Astros | SS | University of Mississippi |
| 43 | Jimmy Gobble | Kansas City Royals | P | John S. Battle HS |
| 44 | Scott Rice | Baltimore Orioles | P | Royal HS |
| 45 | Rob Purvis | Chicago White Sox | P | Bradley University |
| 46 | Chris Duncan | St. Louis Cardinals | 1B | Canyon del Oro HS |
| 47 | Mike Mead | Texas Rangers | P | Soddy Daisy HS |
| 48 | Casey Fossum | Boston Red Sox | P | Texas A&M University |
| 49 | Mike Bynum | San Diego Padres | P | University of North Carolina |
| 50 | Brian Roberts | Baltimore Orioles | SS | University of North Carolina |
| 51 | Nick Trzesniak | San Diego Padres | C | Victor J. Andrew HS |
Compensation Picks
Other notable players
- Carl Crawford, 2nd round, 52nd overall by the Tampa Bay Devil Rays
- Brandon Phillips, 2nd round, 57th overall by the Montreal Expos
- Ryan Doumit, 2nd round, 59th overall by the Pittsburgh Pirates
- Ryan Ludwick, 2nd round, 60th overall by the Oakland Athletics
- John Lackey, 2nd round, 68th overall by the Anaheim Angels
- Justin Morneau, 3rd round, 89th overall by the Minnesota Twins
- Willie Bloomquist, 3rd round, 95th overall by the Seattle Mariners
- Jon Rauch, 3rd round, 99th overall by the Chicago White Sox
- Josh Bard, 3rd round, 100th overall by the Colorado Rockies
- Hank Blalock, 3rd round, 105th overall by the Texas Rangers
- Cody Ross, 4th round, 117th overall by the Detroit Tigers
- Kevin Mench, 4th round, 118th overall by the Texas Rangers
- Ángel Pagán, 4th round, 136th overall by the New York Mets
- Nate Robertson, 5th round, 146th overall by the Florida Marlins
- Joe Saunders, 5th round, 156th overall by the Philadelphia Phillies, but did not sign
- J. J. Putz, 6th round, 185th overall by the Seattle Mariners
- Érik Bédard, 6th round, 187th overall by the Baltimore Orioles
- Shane Victorino, 6th round, 194th overall by the Los Angeles Dodgers
- Aaron Harang, 6th round, 195th overall by the Texas Rangers
- Coco Crisp, 7th round, 222nd overall by the St. Louis Cardinals
- Chris Capuano, 8th round, 238th overall by the Arizona Diamondbacks
- Mark Ellis, 9th round, 271st overall by the Kansas City Royals
- Marlon Byrd, 10th round, 306th overall by the Philadelphia Phillies
- Matt Guerrier, 10th round, 309th overall by the Chicago White Sox
- Greg Dobbs, 10th round, 323rd overall by the Houston Astros, but did not sign
- Lew Ford, 12th round, 379th overall by the Boston Red Sox
- Albert Pujols, 13th round, 402nd overall by the St. Louis Cardinals
- Brandon Lyon, 14th round, 433rd overall by the Toronto Blue Jays
- Garrett Jones, 14th round, 444th overall by the Atlanta Braves
- Jake Peavy, 15th round, 472nd overall by the San Diego Padres
- Matt Diaz, 17th round, 505th overall by the Tampa Bay Devil Rays
- Reed Johnson, 17th round, 523rd overall by the Toronto Blue Jays
- Ryan Raburn, 18th round, 535th overall by the Tampa Bay Devil Rays, but did not sign
- Lyle Overbay, 18th round, 538th overall by the Arizona Diamondbacks
- Scott Hairston, 18th round, 549th overall by the Chicago White Sox, but did not sign
- Noah Lowry, 19th round, 585th overall by the Texas Rangers, but did not sign
- Willie Harris, 24th round, 727th overall by the Baltimore Orioles
- Kevin Tillman, 31st round, 941st overall by the Anaheim Angels
- Jason Frasor, 33rd round, 1145th overall by the Detroit Tigers
- Rich Harden, 38th round, 987th overall by the Seattle Mariners, but did not sign
- Mike Jacobs, 38th round, 1156th overall by the New York Mets
- Kameron Loe, 39th round, 1176th overall by the Philadelphia Phillies, but did not sign
- Adam LaRoche, 42nd round, 1254th overall by the Florida Marlins, but did not sign
- Chris Snyder, 43rd round, 1290th overall by the Seattle Mariners, but did not sign
- Pat Neshek, 45th round, 1337th overall by the Minnesota Twins, but did not sign
NFL players drafted
- Michael Bishop, 44th round, 1328th overall by the Cleveland Indians, but did not sign