| 1st (37th) | Jays | LHP | James Paxton | Ladner, B.C | University of Kentucky |
| 2nd (68th) | Jays | LHP | Jake Eliopoulos | Newmarket, Ont. | Brantford Red Sox/Langley BlazeCanadian National Junior Team |
| 5th (170th) | Cubs | SS | Wes Darvill | Langley, B.C. | Langley Blaze/Canadian National Junior Team |
| 6th (197th) | Phillies | RHP | Steven Inch | Edmonton, Alta. | Vauxhall Academy/Canadian Junior National Team/C-University of Kentucky/C-Midland College |
| 8th (256th) | Brewers | OF | Chad Stang | Surrey, B.C. | Midland College |
| 12th (359th) | Reds | OF | Josh Garton | Guelph, Ont. | Volunteer State College |
| 13th (385th) | Pirates | SS | John Gourley | London, Ont. | Eastern Wayne HS, Goldsboro, NC/C-Eastern Carolina University |
| 14th (413th) | Mariners | OF-3B | Adam Nelubowich | Stony Plain, Alta. | Vauxhall Academy/C-Midland College |
| 15th (445th) | Pirates | C | Peter Bako | Mississauga, Ont. | Connors State College |
| 15th (456th) | Diamondbacks | INF | David Narodowski | Vancouver, BC | University of Kansas |
| 15th (457th) | Dodgers | 1B-3B | Jeff Hunt | Cambridge, Ont. | Intercounty Terriers/Canadian National Junior Team/C-Ohio University |
| 19th (569th) | Reds | LHP | Mitch Clarke | Kitchener, Ont. | Intercounty Terriers |
| 20th (593th) | Mariners | LHP | Jon Hesketh | Langley, B.C. | University of New Mexico |
| 20th (604th) | Rangers | RHP | Jerome Werniuk | Toronto, Ont. | Ontario Prospects/Canadian National Junior Team |
| 22th (668th) | Marlins | SS | Terrence Dayleg | Surrey, BC | Western Kentucky University |
| 25th (749th) | Reds | RHP | Mike Monster | Kelowna, B.C. | Langley Blaze/C-New Mexico Jr. College |
| 25th (756th) | Orioles | LHP | Jay Johnson | Sussex Corner, N.B. | Prairie Baseball Academy/C-Texas Tech |
| 29th (886th) | Brewers | OF | Chandler McLaren | Guelph, Ont. | Intercounty Terriers |
| 30th (903th) | Athletics | OF | Royce Consigli | Welland, Ont. | Niagara Rebels/East Coast Greys/Team Ontario/C-Pittsburgh |
| 30th (911th) | Astros | RHP | Brandon Petite | Glace Bay, N.S. | Vauxhall Academy/Canadian National Junior Team/C-Texas Tech |
| 33th (1007th) | Phillies | RHP | Colin Kleven | Langley, B.C. | Langley Blaze/Team BC/C-Western Iowa |
| 34th (1029th) | Cardinals | RHP | David Kington | Coquitlam, B.C. | Southern Illinois University |
| 34th (1030th) | Jays | SS | Jonathan Fernandez | Toronto/Ft. Lauderdale, Ont./Fla. | Guillford Tech Community College |
| 38th (1160th) | Cubs | OF | Bobby Wagner | Port Coquitlam, B.C. | Panola College |
| 39th (1169th) | Reds | RHP | Paul Barton | Qualicum Beach, B.C. | Parksville Royals/Canadian National Junior Team/C-New Mexico Jr. College |
| 39th (1181th) | Astros | RHP | Rory Young | Chase, B.C. | Langley Blaze/Canadian National Junior Team |
| 40th (1210th) | Jays | OF | Jonathan Gilbert | Quebec City, Que. | Academie Baseball Canada |
| 41th (1230th) | Tigers | C | Larry Balkwill | Chatham, Ont. | Windsor Selects/Canadian National Junior Team/C-Siena College |
| 42th (1230th) | Blue Jays | C | Mike Reeves | Peterborough, Ont. | Ontario Blue Jays/C-Florida Gulf Coast |
| 42th (1272th) | Twins | OF | Marc Bourgeois | Montreal, Que. | Chipolla Jr. College/C-Southern Mississippi |
