Abstract Background Chronic inguinal pain (CIP) can be caused by several factors including musculoskeletal or neurological pathologies as well as by surgical trauma following groin hernia repair. The principal aim of this prospective cohort observational study was to find the incidence and causes of CIP unrelated to surgical trauma 12 months after inguinal hernia repair. Method During sixteen months patients consulting a hernia center for groin-related symptoms were included in the study. Patients were physically evaluated by surgeons and filled out an Inguinal Pain Questionnaire and a Numerical Rating Scale pain-questionnaire. For patients undergoing groin hernia repair, postoperative questionnaires similar to the pre-operative ones were sent out at 12 months. Patients scoring pain on postoperative questionnaires were reevaluated by phone consultation and physical examination. Results 289 patients (78.1%) of 370 repaired patients filled in the postoperative questionnaires. 62 (21.4%) patients scored pain, of these patients 5 (1.7%, 5/289) answered incorrectly in the pain questionnaires and 14 (4.8%, 14/289) had non-surgical trauma causes of pain: 5 musculoskeletal, 4 neurological and 3 other medical pathologies. Conclusion This cohort study found CIP unrelated to surgical trauma in 4.8 % of patients undergoing a groin hernia repair. Most causes of pain unrelated to surgical trauma were musculoskeletal and neurological pathologies. Nearly a third of patients scoring groin pain on pain-questionnaires did not have chronic post-operative pain (CPSP), therefore incidence of CPSP should not be based solely on pain questionnaires. Clinical assessment of patients with pain is necessary to excluded CIP unrelated to surgical trauma.