1999 MLS supplemental draft

| Los Angeles Galaxy{{#tag:ref|#1: New England Revolution → Los Angeles Galaxy. 5 January 1999: Los Angeles Galaxy acquired this first-round selection and a second-round selection in the 1999 MLS College Draft from New England Revolution in exchange for defender Dan Calichman.|group="R1 trade"}} || Gabe Eastman || D || Nashville Metros, Modesto Junior College

| Kansas City Wizards || Brandon Prideaux || D || Seattle Sounders, University of Washington

| San Jose Clash || Adam Frye || D || Tampa Bay Mutiny, UCLA

| MetroStars{{#tag:ref|#4: Tampa Bay Mutiny → D.C. United → MetroStars. 7 February 1999: MetroStars acquired this first-round pick from D.C. United in exchange for a first-round selection in the 2000 Supplemental Draft. The 2000 draft pick was converted to a fourth-round selection in the 2000 MLS SuperDraft when the Supplemental Draft was abolished. On 19 January 1999, D.C. has acquired this first-round pick and a third-round selection (#28) in the 1999 MLS College Draft from Tampa Bay Mutiny in exchange for goalkeeper Scott Garlick.|group="R1 trade"}} || Petter Villegas || M || New Jersey Stallions, Kean University

| Miami Fusion || Dusty Hudock || GK || Seattle Sounders, University of Washington

| Dallas Burn || Kirk Wilson || M || El Paso Patriots, Drake University

| Colorado Rapids{{#tag:ref|#7: MetroStars → Colorado Rapids. 8 March 1998: Colorado Rapids acquired this first-round pick from MetroStars in exchange for forward Steve Rammel.|group="R1 trade"}} || Kevin Anderson || M || Minnesota Thunder, Southern Connecticut State University

| Colorado Rapids || Darren Sawatzky || F || Hershey Wildcats, University of Portland

| Columbus Crew || Michael Butler || F || Western Mass Pioneers, UMass Minutemen

| Los Angeles Galaxy || Orlando Perez || D || Orange County Zodiac

| San Jose Clash{{#tag:ref|#11: D.C. United → San Jose Clash. 28 January 1999: San Jose Clash acquired this first-round pick and a second-round selection in the 1999 MLS College Draft from D.C. United in exchange for financial considerations.|group="R1 trade"}}|| Maxi Viera || M || Detroit Rockers

| Chicago Fire || Tomasz Wygonik || D || Central Jersey Riptide

| New England Revolution || Chris Fox || D || Richmond Kickers, Brown University

| Kansas City Wizards || Ryan Turner || M || University of Notre Dame

| San Jose Clash || Carlos Farias || F || San Diego Flash

| Tampa Bay Mutiny || PASS || ||

| Miami Fusion || Juan Ramos || D || Jacksonville Cyclones, Nova Southeastern University

| Dallas Burn || Gabe Jones || F || Austin Lone Stars, St. Edward's University

| Miami Fusion{{#tag:ref|#19: MetroStars → Miami Fusion. 1 February 1998: Miami Fusion acquired this second-round selection from MetroStars in exchange for a second-round pick (#14) in the 1998 MLS Supplemental Draft.|group="R2 trade"}} || PASS || ||

| Colorado Rapids || David Winner || GK || Miami Fusion, University of Tampa

| Columbus Crew || John DeBrito || M || Kansas City Wizards, Southern Connecticut State University

| Los Angeles Galaxy || John Jones || M || Nashville Metros, Sacramento State

| Dallas Burn{{#tag:ref|#23: D.C. United → Dallas Burn. 18 January 1999: Dallas Burn acquired this second-round selection and a third-round pick (#35) in the 1999 MLS College Draft from D.C. United in exchange for defender Brian Bates.|group="R2 trade"}} || PASS || ||

| Chicago Fire || PASS || ||

| New England Revolution || PASS || ||

| Kansas City Wizards || PASS || ||

| San Jose Clash || Anthony Farace || F || San Diego Flash

| Tampa Bay Mutiny || PASS || ||

| Miami Fusion || PASS || ||

| Dallas Burn || PASS || ||

| MetroStars || Nansha Kalonji || D || Central Jersey Riptide, Ramapo College

| Colorado Rapids || Tim Martin || D || San Jose Clash, Fresno State

| Columbus Crew || Craig Yacks || M || Cincinnati Riverhawks, Yale University

| Miami Fusion{{#tag:ref|#34: Los Angeles Galaxy → Miami Fusion. 1 February 1998: Miami Fusion acquired this third-round selection from Los Angeles Galaxy in exchange for a third-round pick (#26) in the 1998 MLS Supplemental Draft.|group="R3 trade"}} || PASS || ||

| D.C. United || PASS || ||

| Chicago Fire || PASS || ||