Our aim was to perform an exploratory study of various irregular breathing patterns (IBPs) across different sleep stages in patients with acute unilateral lateral medullary infarction (ULMI) and compare them to apparently healthy individuals. Polysomnography (PSG) was analyzed for IBPs, such as periodic breathing, ataxic breathing and tachypnea. IBPs were found in 52 % of healthy and 90 % of ULMI subjects (p = 0.001) and occurred in long (≥ 10 min) episodes in 8% of healthy and 68 % of ULMI (p < 0.001). In healthy subjects, short (< 10 min) episodes of mild to moderate ataxic breathing were observed in wakefulness and light sleep and short episodes of periodic breathing upon sleep onset. In ULMI, the most common IBPs were ataxic and periodic breathing (80 % of patients), followed by shallow tachypnea (28 %). Ataxic breathing predominated in wakefulness, ataxic or periodic breathing in light sleep, while breathing tended to normalize in deep and REM sleep. Considering the IBPs occurring in the healthy group as physiological, probably pathological breathing patterns (tachypnea, long episodes of moderate/severe ataxic or long episodes of periodic breathing) occurred in 67 % of ULMI patients. Our findings suggest that ULMI might exacerbate physiological sleep-stage-dependent breathing pattern irregularities, such as ataxic and periodic breathing, in terms of intensity and duration or might even induce non-physiological IBP, such as shallow tachypnea with sustained hypoxia.