Even though the recommendations for aerobic levels enhancements can promote benefits for the majority of people, the cardiorespiratory fitness (CRF) responses may vary from individual to individual, from non-responder up to high responder after traditional continuous endurance training (CET). In this sense, current studies have been reported the high-intensity interval training (HIIT) to be more effective than CET to improves CRF. Therefore, the aim of this study was to compare the incidence of CRF non-responders between CET and HIIT. Sixty-nine healthy young men (18-30 years old), were randomized in two 8 weeks exercise programs: CET (3-4 times/week, 40 min/day at 70-75% of heart rate reserve (HRR)) or HIIT (3-4 times/week, 40 min/day of 5 x 4:3 sets at 50-90% of HRR). The incidence of CRF non-responders to HIIT was lower in comparison to CET (5.8% vs. 22.8%, respectively, P = 0.045). These results indicates the current guidance for prescribing exercise may not be sufficient to improve CRF for a substantial proportion of healthy young men and the HIIT to be an alternative method to minimize the incidence of CRF non-responders to CET.