Background: The aim of the following study was to identify the effects of a 12-week high-intensity interval training (HIIT) program on the modification of parameters of body composition, functional capacity as well as lipid and glucose homeostasis markers in healthy young people versus older adults. Design: Experimental trial. Methods: Healthy young (YNG, 21 ± 1 years, BMI 26.01 ± 2.64 kg·m-2, n = 10) and older (OLD, 66 ± 5 years, BMI 27.43 ± 3.11 kg·m-2, n = 10) males were subjected to 12 weeks of HIIT. Prior to and immediately after the HIIT program, dual-energy X-ray absorptiometry, dominant leg strength one-repetition maximum (1-RM), maximal oxygen uptake (VO2max) and physical performance tests were performed. Blood samples were also taken. Results: Flexibility (P = 0.000), static balance (P = 0.004), timed up and go test (TUG) (P = 0.015), short physical performance battery (SPPB) (P = 0.005), dominant leg strength 1-RM (P = 0.012), and VO2max (P = 0.000) were better in YNG versus OLD. HIIT improved the % whole-body fat mass (P = 0.031), leg lean mass (P = 0.047), dominant leg strength 1-RM (P = 0.025), VO2max (P = 0.000), fasting cholesterol (P = 0.017) and fasting glucose (P = 0.006). TUG was improved by the training only in the OLD group (P = 0.016), but insulin (P = 0.002) and the homeostasis model assessment - insulin sensitivity (HOMA-IS) (P = 0.000) decreased only in the YNG group. HOMA-IS was correlated positive with BMI (R = 0.474, P = 0.035) and with whole-body fat mass (R = 0.517, P = 0.019). Conclusions: HIIT for 12 weeks improves parameters of body composition, functional capacity and fasting serum lipid and glucose homeostasis markers in healthy young and older participants. Young people are shown as benefiting more.