This is the final version of the article. Available from Springer Verlag via the DOI in this record.PURPOSE: To compare the effects of self-paced high-intensity interval and continuous cycle training on health markers in premenopausal women. METHODS: Forty-five inactive females were randomised to a high-intensity interval training (HIIT; n = 15), continuous training (CT; n = 15) or an inactive control (CON; n = 15) group. HIIT performed 5 × 5 min sets comprising repetitions of 30-s low-, 20-s moderate- and 10-s high-intensity cycling with 2 min rest between sets. CT completed 50 min of continuous cycling. Training was completed self-paced, 3 times weekly for 12 weeks. RESULTS: Peak oxygen uptake (16 ± 8 and 21 ± 12%), resting heart rate (HR) (-5 ± 9 and -4 ± 7 bpm) and visual and verbal learning improved following HIIT and CT compared to CON (P 0.05). No outcome variable changed in the CON group (P > 0.05). CONCLUSIONS: Twelve weeks of self-paced HIIT and CT were similarly effective at improving cardiorespiratory fitness, resting HR and cognitive function in inactive premenopausal women, whereas blood pressure, submaximal HR, well-being and body mass adaptations were training-type-specific. Both training methods improved established health markers, but the adaptations to HIIT were evoked for a lower time commitment.The study was supported by FIFA-Medical Assessment and Research Centre (F-MARC)