Our aim was to estimate the prevalence of nocturnal awakening with headache (NAH) in the population of São Paulo City according to gender, age (20-80 years old) and socioeconomic classes and its relationship to sleep disorders, sleep parameters, anxiety, depression, fatigue, life quality and obesity. We used a population-based survey with a representative three-stage cluster sample. Questionnaires and scales were applied face-to-face, and polysomnography was performed in 1101 volunteers, aged 42 ± 14 years, 55% women. The complaint of NAH occurring at least once a week had a prevalence of 8.4%, mostly in women, obese subjects and those aged 50-59 years-old. We observed associations of NAH with insomnia, restless leg syndrome (RLS), nightmares and bruxism, but not obstructive sleep apnea syndrome. In a logistics regression model, risk factors for NAH were female gender, odds ratio (OR) (95% confidence interval [CI]) 4.5 (2.8-7.3); obesity, OR 1.9 (1.1-3.3); age between 50 and 59 years, OR 2.4 (1.2-4.7); severe anxiety, OR 8.1 (3.6-18.1); RLS, 2.7 (1.2-5.6); and nightmares, 2.2 (1.3-3.7). Our study shows that NAH was highly prevalent in the population of São Paulo and suggests that this phenomenon has specific characteristics with specific risk factors: obesity, RLS and nightmares.