Background The objective of this study was to assess the influence of nocturnal headaches (NH) on subjective sleep parameters prospectively in habitual snorers and their bed partners. Methods We recruited habitual snorers and their bed partners via newspaper articles. The participants completed a semistructured interview, filled in questionnaires about quality of sleep (PSQI), daytime sleepiness (ESS), depression (SDS) and anxiety (SAS) and they kept a 90-day headache and sleep diary. Results Seventy-six snorers (25 female) and 41 bed partners (31 female) completed the study recording a total of 6690 and 3497 diary days, respectively. NH were recorded on 222 (3.3%) and 79 (2.2%) days in 32 (42%) snorers and 17 (41%) bed partners, respectively. Snorers with NH showed significantly higher PSQI (5 ± 3 vs. 4 ± 2, p = 0.004), SAS (38 ± 11 vs. 31 ± 10, p = 0.011) and SDS scores (39 ± 12 vs. 34 ± 10, p = 0.048) than snorers without NH. For bed partners with NH we found a significant female predominance (sex ratio f:m = 16:1 vs. 12:12, p = 0.005) and significantly higher SAS scores (38 ± 6 vs. 33 ± 8, p = 0.030) compared with bed partners without NH. The subjective quality of sleep in habitual snorers ( p < 0.001) as well as their bed partners ( p = 0.017) was negatively influenced by NH, but not total sleep time. Discussion NH occurred in around 40% of snorers and their bed partners at least once during the 90-day observation period. Our results confirmed a negative impact on the subjective quality of sleep in both groups.