The aim of study was to evaluate the effects of interval training performed in hypoxia on aerobic capacity and second ventilatory threshold in young, untrained men. Participants (n = 48) were randomly divided into a control group and two groups performing the same interval training (three times a week for 4 weeks) in normoxia (200 m asl) (NT) and in hypoxia (IHT) (3000 m asl, FIO2 = 14.4%). In the incremental test, maximal oxygen uptake (VO2max) was measured and the first (VT1) and second (VT2) ventilatory thresholds and the maximal power output (Pmax) were determined for each participant. The training workloads of the efforts corresponded to the workload at VT2 (effort) and VT1 (active recovery). Training in both normoxia and hypoxia significantly increased absolute VO2max (p = 0.02, ES = 0.51 and p = 0.002, ES = 0.47, respectively). In comparison to NT, only IHT significantly (p < 0.001; ES = 0.80) improved Pmax, as well as power at VT2 (p = 0.02; ES = 0.78). The applied IHT was effective in improving Pmax and power at VT2, which was not observed after training in normoxia.