Short pauses or "transition-periods" at the end of expiration and prior to subsequent inspiration are commonly observed during sleep in humans. However, the role of transition periods in regulating ventilation during physiological challenges such as partial airway obstruction (PAO) has not been investigated. Twenty-nine obstructive sleep apnea patients and eight controls underwent overnight polysomnography with an epiglottic catheter. Sustained-PAO segments (increased epiglottic pressure over ≥5 breaths without increased peak inspiratory flow) and unobstructed reference segments were manually scored during apnea-free non-REM sleep. Nasal pressure data was computationally segmented into inspiratory (TI, shortest period achieving 95% inspiratory volume), expiratory (TE, shortest period achieving 95% expiratory volume), and inter-breath transition period (TTrans, period between TE and subsequent TI). Compared with reference segments, sustained-PAO segments had a mean relative reduction in TTrans (-24.7±17.6%, P<0.001), elevated TI (11.8±10.5%, P<0.001), and a small reduction in TE (-3.9±8.0, P≤0.05). Compensatory increases in inspiratory period during PAO are primarily explained by reduced transition period and not by reduced expiratory period.