The purpose of this study was to compare the effects of intra-set rest intervals (ALT) and traditional resistance (STD) training in hypertrophic resistance training. 22 males (25 +/- 5yrs, 179.71 +/- 5.0cm, 82.1 +/- 10.6kg, 13.6 +/- 4.3% fat, 6.5 +/- 4.5yrs training) were matched according to baseline characteristics and randomly assigned to a STD or ALT 12 week hypertrophic training protocol. Body composition, strength (1RM bench and squat); power (60% 1RM bench and squat); and vertical jump were assessed at baseline, 4, 8, and 12 weeks. Muscle biopsy for myosin heavy chain (MHC) was performed pre and post training. A 2 x 4 (Group x Time) ANOVA was used to assess changes in body composition. A 2 x 4 (Group x Time) ANCOVA covaried by baseline performance measures was used to assess differences in strength and power characteristics. A 2 x 2 (Group x Time) ANCOVA covaried for baseline percentage MHC was used to determine differences pre and post training. Both groups experienced increases in FFM with no differences between groups (62.6 +/- 7.9, 63.4 +/- 7.6, 64.2 +/- 7.4, 64.2 +/- 7.5kg; p>0.05). No time effects were noted in percent fat (13.6 +/- 4.3, 14.1 +/- 4.7, 14.0 +/- 4.6, 14.3 +/- 4.6%fat; p>0.05). Increase in FFM was associated with a decrease in MHCIIX, (ALT, -37.9 +/- 24.1%; STD, -23.4 +/- 23.8%; p = 0.001) and an increase in MHCIIA (ALT, 32.0 +/- 28.8%; STD, 25.4 +/- 29.1%; p = 0.001) with no difference between groups. A significant interaction was observed with the ALT group experiencing greater gains in both 1RM bench (STD 104.1 +/- 27.6, 102.7 +/- 29.0, 107.0 +/- 25.3, 113.2 +/- 27.3; ALT 110.9 +/- 20.1, 117.5 +/- 23.7, 120.8 +/- 22.6, 126 +/- 22.8; p<0.05) and 1RM squat (STD 123.3 +/- 39.3, 139.6 +/- 38.8, 160.2 +/- 36.1, 171.8 +/- 34.5; ALT 130.1 +/- 25.1, 152.6 +/- 24.8, 179.8 +/- 24.5, 193.9 +/- 24.2kg; p<0.05). The ALT group experienced greater gains in power in both the bench (STD 560 +/- 122, 541 +/- 105, 572 +/- 122, 593 +/- 135W; ALT 575 +/- 102, 586 +/- 123, 646 +/- 103, 658 +/- 113W; p<0.05) and vertical jump (STD 1378 +/- 237, 1418 +/- 214, 1452 +/- 210, 1470 +/- 215W; ALT 1389 +/- 179, 1434 +/- 152, 1470 +/- 149, 1537 +/- 150W;p<0.05), with gains in squat power approaching significance (STD 625 +/- 245, 704 +/- 233, 723 +/- 227, 830 +/- 232W; ALT 632 +/- 171, 734 +/- 179, 783 +/- 188, 914 +/- 207W; p<0.10). The use of intra-set rest intervals in programs designed to elicit hypertrophy results in greater gains in strength and power with no significant difference in lean mass or MHC composition after a 12 week resistance training program designed to elicit hypertrophy.