The aim of the study was to investigate ACTN3 (α-actinin-3) and AMPD1 (adenosine monophosphate deaminase) polymorphism and genotype combinations in Bulgarian athletes competing in various sports and the relation to peak power output. A mixed group of athletes (n = 52) competing at national and international level and a matching genetic control group (n = 109) of volunteers were recruited. Participants were genotyped for ACTN3 and AMPD1 by polymerase chain reaction. There were no significant differences in ACTN3 genotype distribution between athletes performing Wingate test (38% RR, 46% RX, 16% XX) and controls (41.2% RR, 46% RX, 12.8% XX). AMPD1 distribution was (73% CC, 27% CT, 0% TT) and in controls (73.2% CC, 25% CT, 1.8% TT). Athletes performing Wingate test showed equal 33% frequency of RR/CC and RX/CC combination, and 12% RX/CT. Significantly higher (P < 0.05) peak power output (11.10 W kg-1) was found in athletes with RX/CT combination compared to other combinations (range: 8.83-9.71 W kg-1) and in R-power (RR + RX) and C-power (CC + CT) dominant models (9.91 W kg-1). Mean power was higher (P < 0.05) in RX/CT combination (8.93 W kg-1) compared to RR/CC (7.75 W kg-1) and RR/CT (7.95 W kg-1). In conclusion, the low frequency of T AMPD1 allele in Bulgarian athletes might indicate that this mutant allele is related to the physical performance. The prevalence of R ACTN3 and C AMPD1 alleles suggests that they could contribute to anaerobic performance. Higher peak power in Wingate test is associated with RX/CT genotype combination and R-and C-power dominant models.