The purpose of the presented study was to compare acute and post-exercise differences in cardiorespiratory, metabolic, cardiac autonomic, inflammatory and muscle damage responses to high-intensity interval exercise (HIIT) between endurance and sprint athletes. The study group consisted of sixteen highly-trained males (age 22.1 ± 2.5 years) participating in endurance (n = 8) or sprint (n = 8) sporting events. All the participants underwent three exercise sessions: short HIIT (work interval duration 30s), long HIIT (3min) and constant load exercise (CE). The exercise interventions were matched for mean power, total time and in case of HIIT interventions also for work-to-relief ratio. The acute cardiorespiratory (HR, V̇O₂, RER) and metabolic (lactate) variables as well as the post-exercise changes (up to 3 h) in the heart rate variability, inflammation (interleukin-6, leucocytes) and muscle damage (creatine kinase, myoglobin) were monitored. Endurance athletes performed exercise interventions with moderately (CE) or largely (both HIIT modes) higher mean V̇O₂. These differences were trivial/small when V̇O₂ was expressed as a percentage of V̇O_2max. Moderately to largely lower RER and lactate values were found in endurance athletes. Markers of cardiac autonomic regulation, inflammation and muscle damage did not reveal any considerable differences between endurance and sprint athletes. In conclusions, endurance athletes were able to perform both HIIT formats with increased reliance on aerobic metabolic pathways although exercise intensity was identical in relative terms for all the participants. However, other markers of the acute and early post-exercise physiological response to these HIIT interventions indicated similarities between endurance and sprint athletes.