The aim of this paper was to assess the prevalence of morning headaches in the Austrian general population and to analyse their relationship to daytime functioning and quality of sleep. In a nationwide survey, we recruited 1000 adults (478 men, 522 women, age over 14 years). For this study, we selected all subjects with self-reported morning headaches as well as controls matched for age, sex, size of hometown, level of education and marital status. Forty-eight persons reported morning headaches making a prevalence of 5% in the Austrian general population. Compared to controls, subjects with morning headaches reported more often daytime sleepiness (50% vs. 18.8%, p = 0.003), difficulties in staying awake (47.9% vs. 18.8%, p = 0.005) and falling asleep involuntarily (29.2% vs. 8.3%, p = 0.019). Moreover, they reported a longer sleep onset latency (26.5 ± 27.5 vs. 13.5 ± 13.5 min, p = 0.005), and more often sleep disturbances (58.3% vs. 14.6%, p < 0.001), tossing and turning around during the night (50.0% vs. 8.0%, p < 0.001), problems with sleep maintenance (64.6% vs. 22.9%, p < 0.001) and the symptom of restless legs (20.8% vs. 2.1%, p = 0.01). In addition, subjects with morning headaches felt less often refreshed in the morning (18% vs. 51%, p < 0.001) and reported regular use of medication more often (64.6% vs. 29.2%, p = 0.001) than controls. After correction for multiple testing, the differences in sleep maintenance, sleep disturbances and regular use of medication remained statistically significant. In conclusion, this is the first Austrian population-based controlled study to show that morning headaches afflict one out of 20 persons and are related to self-reported sleep problems.