The purpose of this study was to investigate the effect of complex training (combination of plyometrics and multi-joint resistance exercises) on muscle damage and performance indices for 96 hours post-exercise. Participants (young, healthy men) were randomly assigned to one of three groups: a) Complex training group with high-intensity resistance exercise(CH, N=8, plyometrics: 100 total foot contacts; resistance exercise: 90% 1RM, 3 sets/exercise of 3 repetitions each), b) Complex training group with low-intensity resistance exercise(CL, N=8, plyometrics: 100 total foot contacts; resistance exercise: 50% 1RM, 3 sets of 8 repetitions each), and c) a control group (C=8). Delayed onset muscle soreness (DOMS), knee range of motion (KROM), thigh circumferences as well as isometric peak torque, squat jump (SQ) and countermovement jump (CJ) were determined at rest, immediately post-exercise as well as 24h, 48h, 72h, and 96h within recovery. CH and CL increased (p<.05) DOMS (peaked at 24h post-exercise), thigh circumference (peaked at 24h post-exercise) while decreased (p<.05) KROM compared to resting values. The two exercise groups induced a marked (p<.05) decline in SQ (by 20% approximately at 24 h post exercise and remained below basal values throughout recovery in both groups) and CJ (until 48h in CH and until 24h in CL) compared to resting values and the C group. Isometric strength declined (p< .05) for both exercise groups until 24h of recovery and returned to baseline thereafter. The results of this investigation suggest that performing an acute bout of complex training may induce transient muscle damage and marked performance deterioration for as long as 24-72h in an intensity dependent manner.