The application of ambulatory electrocardiography to identify obstructive sleep apnea syndrome (OSAS) patients was evaluated using time-domain and frequency-domain analyses of heart rate variability (HRV). For this, overnight sleep pattern was investigated in 95 individuals (48 OSAS(+) patients and 47 OSAS(-) controls) by polysomnography and 24-h ambulatory electrocardiography. Apnea scores were calculated using two different HRV analyses. Average age and body mass index, and percentages of men and of patients with history of hypertension and/or diabetes were higher in study group as compared with control group. PNN50(night), SDNNI(day-night) and SDNNI(day-night) in time-domain analysis were more sensitive than other indices. In frequency-domain analysis, mean night-time total power, night-time VLF power, night-time LF power, and the difference between these measures in day and night were significantly higher in study group. LF/HF ratio was also significantly higher in study group in day-time or night-time with a significant difference (P < 0.05) between day and night. At sleep apnea risk score >4, sensitivity, specificity, and positive predictive value were, respectively, 81.25, 46.81, and 64.21%. At sleep apnea risk scores >5, 6, or 7, the specificity increased, while the sensitivity and positive predictive value decreased. In conclusion, time-domain and frequency-domain HRV analyses are useful methods for OSAS screening, and the frequency-domain analysis is more sensitive.