Background: Hidradenitis suppurativa (HS) is a chronic autoinflammatory skin condition and is associated with several comorbidities. Previous studies report variable prevalence rates of HS, depending on the methodology. However, the exact prevalence remains unknown. Objectives: To estimate the prevalence of HS in a large population-based cohort in the Northern Netherlands, and to compare patients with HS to the general population, investigate characteristics and identify potential associated comorbidities. Methods: Data were collected through a cross-sectional survey-based study within the Lifelines Cohort Study (n = 167 729), based on the general population located in the Northern Netherlands. A digital self-reported questionnaire was developed consisting of validated questions for determining HS. Results: Among 56 084 respondents, the overall prevalence of HS was 2.1% [95% confidence interval (CI) 2.0–2.2]. The respondents with HS had lower socioeconomic status than the controls (P < 0.001) and more frequently currently smoked (P < 0.001). Several new significant associations in patients with HS were revealed, such as fibromyalgia (OR 2.26, 95% CI 1.64–3.11), irritable bowel syndrome (OR 1.63, 95% CI 1.18–2.26), chronic fatigue syndrome (OR 1.72, 95% CI 1.06–2.78) and migraine (OR 1.48, 95% CI 1.11–1.96). Fibromyalgia and chronic fatigue syndrome remained significantly associated with HS in the multivariate analysis after adjusting for age, sex, body mass index, smoking status and socioeconomic status. Conclusions: Our study showed a higher prevalence of HS in the Northern Netherlands compared with the overall estimated prevalence of 1% and identified several new associated comorbidities.