| 1 | Miilpalu Matteus | 2002 | EST Ujumise Spordiklubi | 00'54''27 | 567 |  |  | |
50m 26.11 (26.11) 100m 54.27 (28.16) [54.27] |
| 2 | Medzhidov Mayid | 2002 | RUS Ska, St. Petersburg | 00'54''90 | 548 | | | |
50m 26.57 (26.57) 100m 54.90 (28.33) [54.90] |
| 3 | Solodov Demid | 2003 | EST Spordiklubi Energia | 00'55''00 | 545 | | | |
50m 26.35 (26.35) 100m 55.00 (28.65) [55.00] |
| 4 | Kuzmin Sergei | 2002 | EST Argo Ujumisklubi | 00'55''55 | 529 | | | |
50m 26.18 (26.18) 100m 55.55 (29.37) [55.55] |
| 5 | Oper Georg | 2002 | EST Tartu Ujumisklubi | 00'56''15 | 512 | | | |
50m 26.82 (26.82) 100m 56.15 (29.33) [56.15] |
| 6 | Tsvetkov Pavel | 2003 | RUS Ska, St. Petersburg | 00'56''78 | 495 | | | |
50m 26.75 (26.75) 100m 56.78 (30.03) [56.78] |
| 7 | Tammer Toomas Tanel | 2003 | EST Tartu Ujumisklubi | 00'56''85 | 493 | | | |
50m 27.73 (27.73) 100m 56.85 (29.12) [56.85] |
| 8 | Zvejnieks Haralds | 2003 | LAT Bjss Ridzene-Olimpiskais Sc | 00'58''21 | 460 | | | |
50m 27.63 (27.63) 100m 58.21 (30.58) [58.21] |
| 9 | Glazkov Vladislav | 2003 | RUS Ska, St. Petersburg | 00'58''54 | 452 | | | |
50m 27.67 (27.67) 100m 58.54 (30.87) [58.54] |
| 10 | Filippov Aleksandr | 2002 | EST Argo Ujumisklubi | 00'58''70 | 448 | | | |
50m 27.87 (27.87) 100m 58.70 (30.83) [58.70] |
| 11 | Petrov Dmitri | 2003 | EST Spordiklubi Dilan | 00'58''83 | 445 | | | |
50m 27.90 (27.90) 100m 58.83 (30.93) [58.83] |
| 12 | Polyakov Egor | 2002 | RUS Ska, St. Petersburg | 00'59''21 | 437 | | | |
50m 27.82 (27.82) 100m 59.21 (31.39) [59.21] |
| 13 | Koboshev Vadim | 2003 | EST Maardu Ujumisklubi | 00'59''65 | 427 |
| 14 | Valkrusman Andreas | 2003 | EST Argo Ujumisklubi | 00'59''72 | 426 | | | |
50m 28.98 (28.98) 100m 59.72 (30.74) [59.72] |
| 15 | Bobkovs Daniels | 2003 | LAT Bjss Ridzene-Ziepniekkalns | 01'00''41 | 411 | | | |
50m 28.61 (28.61) 100m 1:00.41 (31.80) [1:00.41] |
| 16 | Muraviev Danila | 2003 | RUS Ska, St. Petersburg | 01'00''81 | 403 | | | |
50m 28.58 (28.58) 100m 1:00.81 (32.23) [1:00.81] |
| 17 | Beditski Aleksandr | 2002 | EST Spordiklubi Garant | 01'01''88 | 383 | | | |
50m 29.12 (29.12) 100m 1:01.88 (32.76) [1:01.88] |
| 18 | Ruotsalainen Patrik | 2002 | EST Ujumise Spordiklubi | 01'01''95 | 381 | | | |
50m 28.77 (28.77) 100m 1:01.95 (33.18) [1:01.95] |
| 19 | Kivari Marten-Hugo | 2003 | EST Tartu Ujumisklubi | 01'03''86 | 348 | | | |
50m 30.85 (30.85) 100m 1:03.86 (33.01) [1:03.86] |
| 20 | Garniks Deniss | 2003 | LAT Bjss Ridzene-Ziepniekkalns | 01'03''92 | 347 | | | |
50m 29.71 (29.71) 100m 1:03.92 (34.21) [1:03.92] |
| 21 | Konev Arsenii | 2003 | EST Spordiklubi Garant | 01'05''09 | 329 | | | |
50m 31.05 (31.05) 100m 1:05.09 (34.04) [1:05.09] |
| 22 | Rannik Ranel | 2003 | EST Kalevi Ujumiskool | 01'05''50 | 322 | | | |
50m 30.50 (30.50) 100m 1:05.50 (35.00) [1:05.50] |
| 23 | Sokolov Mikhail | 2002 | RUS Ska, St. Petersburg | 01'05''56 | 322 | | | |
50m 28.83 (28.83) 100m 1:05.56 (36.73) [1:05.56] |
| 24 | Tammeniit Karl Mattias | 2002 | EST Parnu Spordikool | 01'07''62 | 293 | | | |
50m 32.32 (32.32) 100m 1:07.62 (35.30) [1:07.62] |
| 25 | Kulesa Maksim | 2003 | EST Spordiklubi Garant | 01'08''33 | 284 | | | |
50m 31.96 (31.96) 100m 1:08.33 (36.37) [1:08.33] |
| 26 | Vegeris Francis Daniels | 2003 | LAT Bjss Ridzene-Olimpiskais Sc | 01'09''31 | 272 | | | |
50m 33.25 (33.25) 100m 1:09.31 (36.06) [1:09.31] |
| 27 | Murro Marco | 2002 | EST Hiiu Hueljes | 01'13''38 | 229 | | | |
50m 34.62 (34.62) 100m 1:13.38 (38.76) [1:13.38] |
| 28 | Palmov Egor | 2003 | EST Spordiklubi Garant | 01'14''40 | 220 | | | |
50m 36.05 (36.05) 100m 1:14.40 (38.35) [1:14.40] |
