Background: It is unclear if childhood trauma (CT) is an independent risk factor of adult chronic physical disorders or whether its impact is (also) due to underlying poorer mental health. Methods: Data were obtained from baseline measurements among 13,489 respondents of the Netherlands Mental Health Survey and Incidence Study-1 and -2, cohort studies of the Dutch general population aged 18–64 years. We used a childhood trauma questionnaire measuring emotional, psychological, physical or sexual trauma before the age of 16. Lifetime mood, anxiety and substance use disorders were assessed with the Composite International Diagnostic Interview version 1.1 and 3.0. A standard self-report checklist was used to assess a broad range of chronic physical disorders treated by a medical doctor in the previous 12 months. Results: Respondents with a history of CT (N = 4054) suffered significantly more often from digestive (OR: 1.89–2.95), musculoskeletal (OR: 1.21–1.75) and respiratory disorders (OR: 1.39–1.91) and migraine (OR: 1.42–1.66). We found indirect associations between CT and digestive, musculoskeletal and respiratory disorders through lifetime mood (54%, 52% and 48% respectively), anxiety (44%, 55% and 44% respectively) and substance use disorders (33%, 23% and 38% respectively). Mood (69%) and anxiety disorders (67%) also impacted the relationship with migraine. Conclusions: CT predicts the development of adult physical disorders, even after controlling for sociodemographic and lifestyle factors. This association is substantially influenced by mental health disorders. Treatment programs for CT should include interventions aimed at enhancing both mental and physical health.