The healthcare sector is a major contributor of greenhouse gas emissions, and reduction and proper sorting of healthcare waste is essential to achieve sustainable healthcare. This study aimed to characterize the quantity and composition of pharmaceutical waste from a major Danish hospital. Pharmaceutical waste was collected from Odense University Hospital, including departments located in both Odense and Svendborg. The average daily production of pharmaceutical waste was 1150 g/day in Odense and 5967 g/day in Svendborg, with the operating rooms in Svendborg contributing 3143 g/day. The amount and composition of pharmaceutical waste varied greatly between departments, but some common patterns were identified. Propofol accounted for about one third of the pharmaceutical waste obtained from operating rooms. Antibiotics for systemic use constituted a significant proportion of the pharmaceutical waste from several departments, and were the therapeutic group from which most different drugs were identified. Paracetamol accounted for 33.5% of the discarded tablets/capsules in Odense and 12.6% in Svendborg. Medications dispensed by automated dose dispensing accounted for a significant proportion of the discarded tablets/capsules in departments using this service. This study highlights some key areas for reduction and management of pharmaceutical waste, and contributes to the currently limited evidence within this area.