Sleep disordered breathing (SDB) is an independent risk factor for cardiovascular disease. It is known to be associated more frequently with men than women, particularly in the premenopausal age range. The goal of this study is to evaluate gender differences among Korean patients diagnosed with SBD. This study included 309 patients who visited our Sleep Clinic due to sleep-related symptoms and were diagnosed with SDB by overnight polysomnography (PSG). We analyzed age, gender, body mass index, various PSG indices including sleep stages, apnea-hypopnea index (AHI) and AHI ratio in rapid eye movement (REM) versus non-REM (NREM) sleep stages (R:N ratio). Of those 309 patients diagnosed with obstructive sleep apnea, 217 (70.2%) were men (mean age 51.05 ± 12.64 years) and 92 (29.8%) were women (mean age 64.53 ± 10.43 years). The mean AHI during total sleep time was 30.34 ± 21.17 in men and 21.47 ± 17.14 in women (P < 0.001). The AHI in NREM sleep was higher in men than in women (30.97 ± 22.39 versus 20.19 ± 18.17, P < 0.001), whereas the AHI in REM sleep was not significantly different between men and women (25.73 ± 21.61 versus 28.00 ± 21.76, P = 0.402). REM SDB with R:N ratio higher than 2.0 was more frequently observed in women than in men, 34.8% (32/92) of women, compared with 11.9% (26/217) in men (P < 0.001). Interestingly, the mean R:N ratio tended to decrease with increasing age in women, but remained relatively constant in men. The prevalence of REM SDB was higher in women than in men, and the gender difference was the most prominent in women with the age < 60 years old compared to age-matched and older men or women > 60 years old. These findings suggest the possibility of different pathophysiologic mechanisms of SDB between genders and also between NREM versus REM sleep, which can be partly explained by the influence of female sex hormones.