1999 MLS College Draft#Round 3

| D.C. United{{#tag:ref|#1: New England Revolution → MetroStars → D.C. United. 4 February 1998: As third part of three-team trade with New England, D.C. United acquired this first-round selection from MetroStars to fulfill "future considerations" in the Raul Diaz Arce trade. 4 February 1998: As second part of three-team trade with D.C. United, MetroStars acquired this first-round selection and defender Alexi Lalas from New England Revolution in exchange for Raul Diaz Arce.|group="R1 trade"}} || Jason Moore || M || University of Virginia

| Miami Fusion{{#tag:ref|#2: Kansas City Wizards → Miami Fusion. 6 February 1999: Miami Fusion acquired this first-round selection from Kansas City Wizards in exchange for a first-round pick (#5) in the 1999 MLS College Draft and a first-round pick in the 2000 MLS SuperDraft.|group="R1 trade"}} || Jay Heaps || M || Duke University

| San Jose Clash || Richard Mulrooney || F || Creighton University

| Dallas Burn{{#tag:ref|#4: Tampa Bay Mutiny → Chicago Fire → Dallas Burn. 7 February 1999: Dallas Burn acquired this first-round pick and the #12 selection in the 1999 College Draft from Chicago Fire in exchange for midfielder Dema Kovalenko. On 29 June 1998, Chicago had acquired this first-round pick and midfielder Josh Keller from Tampa Bay Mutiny in exchange for defender Jorge Salcedo.|group="R1 trade"}} || Lazo Alavanja || M || Indiana University

| Kansas City Wizards{{#tag:ref|#5: Miami Fusion → Kansas City Wizards. 6 February 1999: Kansas City Wizards acquired this first-round pick and a first-round pick in the 2000 MLS SuperDraft from Miami Fusion in exchange for a first-round selection (#2) in the 1999 MLS College Draft.|group="R1 trade"}}|| Chris Brown || F || University of Portland

| Dallas Burn || Bobby Rhine || F || University of Connecticut

| MetroStars || John Wolyniec || F || Fordham University

| Colorado Rapids || Andrew Mittendorf || F || Lehigh University

| Columbus Crew || Matt Chulis || D || University of Virginia

| Los Angeles Galaxy || Tony Soto || D || Southern Methodist University

| Chicago Fire{{#tag:ref|#11: D.C. United → Chicago Fire. 6 January 1998: Chicago Fire acquired this first-round pick, a second-round pick (#23) in the 1999 College Draft (both picks originally "future considerations"), and midfielder Jesse Marsch from D.C. United in exchange for a second-round selection (#14) in the 1998 MLS College Draft and forward A.J. Wood.|group="R1 trade"}} || Evan Whitfield || D || Duke University

| Dallas Burn{{#tag:ref|#12: Chicago Fire → Dallas Burn. 7 February 1999: Dallas Burn acquired this first-round pick and the #4 selection in the 1999 College Draft from Chicago Fire in exchange for midfielder Dema Kovalenko.|group="R1 trade"}} || Paul Broome || M || Southern Methodist University

| Los Angeles Galaxy{{#tag:ref|#13: New England Revolution → Los Angeles Galaxy. 5 January 1999: Los Angeles Galaxy acquired this second-round selection and a first-round pick in the 1999 MLS Supplemental Draft from New England Revolution in exchange for a defender Dan Calichman.|group="R2 trade"}} || Seth George || F || UCLA

| Kansas City Wizards || John Wilson || D || Clemson University

| San Jose Clash || Wojtek Krakowiak || F || Clemson University

| MetroStars{{#tag:ref|#16: Tampa Bay Mutiny → New England Revolution → MetroStars. 7 February 1999: MetroStars acquired this second-round selection from New England Revolution in exchange for two second round selections in the 2000 MLS SuperDraft. Earlier the same day, New England had acquired this second-round pick from Tampa Bay Mutiny in exchange for a fifth-round pick in the 2000 MLS SuperDraft (originally a second-round selection in the canceled 2000 MLS Supplemental Draft).|group="R2 trade"}} || Kevin Knight || M || James Madison University

| D.C. United{{#tag:ref|#17: Miami Fusion → D.C. United. 5 December 1998: D.C. United acquired this second-round pick and a first-round selection in the 2000 MLS SuperDraft from Miami Fusion in exchange for a second-round pick (#19) in the 1999 MLS College Draft and midfielder Mario Gori.|group="R2 trade"}} || Keith Beach || M || University of Maryland

| Columbus Crew{{#tag:ref|#18: Dallas Burn → Miami Fusion → Columbus Crew. 6 February 1999: Columbus Crew acquired this second-round pick and defender Matt Kmosko from Miami Fusion in exchange for a first-round selection in the 2000 MLS SuperDraft. On Date Needed, Miami had acquired this second-round selection from Dallas Burn in exchange for a third-round pick (#25) in the 1998 MLS College Draft. More information needed.|group="R2 trade"}} || Jeff Bilyk || M || Clemson University

| Miami Fusion{{#tag:ref|#19: MetroStars → D.C. United → Miami Fusion. 5 December 1998: Miami Fusion acquired this second-round pick and Mario Gori from D.C. United in exchange for a second-round pick (#17) in the 1999 MLS College Draft and a first-round pick in the 2000 MLS SuperDraft (originally a first-round selection in the canceled 2000 MLS College Draft). 4 February 1998: As first part of three-team trade with New England Revolution, D.C. United acquired this second-round pick and future considerations (New England's first-round pick (#1) in the 1999 MLS College Draft) from MetroStars in exchange for Raul Diaz Arce.|group="R2 trade"}} || Jeremy Aldrich || D || Butler University

| Colorado Rapids || Tom Poltl || M || UCLA

| San Jose Clash {{#tag:ref|#21: Columbus Crew → D.C. United → San Jose Clash. 28 January 1999: San Jose Clash acquired this second-round pick and a first-round selection in the 1999 MLS Supplemental Draft from D.C. United in exchange for financial considerations. On Date Needed, D.C. had acquired this second-round selection from Columbus Crew in exchange for a second-round pick (#24) in the 1998 MLS College Draft. More information needed.|group="R2 trade"}} || Jamie Clark || D || Stanford University

| Los Angeles Galaxy || Sam Franklin || M || University of Virginia

| Chicago Fire{{#tag:ref|#23: D.C. United → Chicago Fire. 6 January 1998: Chicago Fire acquired this second-round pick, a first-round pick (#11) in the 1999 College Draft (both picks originally "future considerations"), and midfielder Jesse Marsch from D.C. United in exchange for a second-round selection (#14) in the 1998 MLS College Draft and forward A.J. Wood.|group="R2 trade"}} || Greg Sutton || GK || St. Lawrence University

| Dallas Burn{{#tag:ref|'#24: Pick originally belonged to Chicago Fire. → Dallas Burn.|group="R2 trade"}} || Darren Warham || D || Lynn University

| New England Revolution || Leighton O'Brien || M || University of San Diego

| Kansas City Wizards || Kevin Kalish || D || St. Louis University

| San Jose Clash || Todd Duncan || D || San Jose State University

| D.C. United{{#tag:ref|#28: Tampa Bay Mutiny → D.C. United. 19 January 1999: D.C. United acquired this third-round selection and a first-round pick (#4) in the 1999 MLS Supplemental Draft from Tampa Bay Mutiny in exchange for goalkeeper Scott Garlick.|group="R3 trade"}} || David Hayes || F || Wingate University

| MetroStars{{#tag:ref|#29: Miami Fusion → MetroStars. 30 June 1998: MetroStars acquired this third-round selection from Miami Fusion in exchange for defender Matt Knowles.|group="R3 trade"}} || Jim Manganello || M || Wheaton College

| Dallas Burn || Andrew Parrish || D || Indiana University

| MetroStars || Eric Kvello || F || Georgetown University

| Colorado Rapids || Bobby Meyer || D || Dartmouth College

| Columbus Crew || Randy Merkel || D || University of Maryland

| Los Angeles Galaxy || PASS || ||

| Dallas Burn{{#tag:ref|#35: D.C. United → Dallas Burn. 18 January 1999: Dallas Burn acquired this third-round selection and a second-round pick in the 1999 MLS Supplemental Draft from D.C. United in exchange for defender Brian Bates.|group="R3 trade"}} || Aaron Lewis || M || Western Baptist College

| Chicago Fire || Stefani Miglioranzi || M || St. John's University