The aim of this study was to investigate changes of interleukin-6 (IL-6), total antioxidant capacity (TAC) and muscle damage markers (creatine kinase (CK), myoglobin and lactate dehydrogenase (LDH)) in response to three different high-intensity interval training (HIIT) protocols of identical external work. Twelve moderately-trained males participated in the three HIIT trials which consisted of a warm-up, followed by 12 min of 15 s, 30 s or 60 s HIIT sequences with the work/rest ratio 1. The biochemical markers of inflammation, oxidative stress and muscle damage were analysed POST, 3 h and 24 h after the exercise. All HIIT protocols caused an immediate increase in IL-6, TAC, CK, myoglobin and LDH. The most pronounced between-trials differences were found for the POST-exercise changes in IL-6 (Effect size ± 90% confidence interval: 1.51 ± 0.63, 0.84 ± 0.34 and 1.80 ± 0.60 for the 15s/15s, 30s/30s and 60s/60s protocol, respectively) and myoglobin (1.11 ± 0.29, 0.45 ± 0.48 and 1.09 ± 0.22 for the 15s/15s, 30s/30s and 60s/60s protocol, respectively). There were no substantial between-trial differences in other biochemical variables. In conclusion, the 15s/15s and 60s/60s protocols might be preferred to the 30s/30s protocols in order to maximize the training stimulus.