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OBJECTIVES This study aimed to examine the effects of different recovery durations on self-selected running velocities, physiological responses, and ratings of perceived exertion (RPE) in a commonly used high intensity interval training (HIIT) protocol. DESIGN & METHODS Twelve trained runners performed an incremental treadmill exercise test to determine maximal oxygen uptake (V˙O2max) and heart rate (HRmax). In four subsequent visits, participants performed a HIIT session comprising six 4-min work intervals, in which the recovery duration between work intervals equalled either a fixed (1MIN, 2MIN, 3MIN) or a self-selected duration (ssMIN). HIIT sessions were run on a non-motorized treadmill, and were performed under isoeffort conditions. RESULTS Mean running velocity was significantly higher in 3MIN compared with all other protocols, and higher in ssMIN compared with 2MIN. No significant differences in time spent ≥90% and 95% V˙O2max, or ≥90% and 95% HRmax were evident between the four protocols. RPE responses were similar across and within the protocols showing a gradual increase with each progressive interval. CONCLUSION In a self-paced HIIT session of six 4-min work intervals, the length of recovery durations had a limited effect on the total physiological strain endured in the training. However, running velocities were higher when participants received the longest recovery period (3MIN). Longer recovery durations may facilitate a higher external training load (faster running), whilst maintaining a similar internal training load (physiological stimulus), and may therefore allow for greater training adaptations.