Amputation surgery in pinniped rehabilitation centers is a feasible procedure when animals are presented with open fractures, osteomyelitis, and/or infectious arthritis of the flippers that appear to be refractory to medical treatment. From 2011 to 2017, the Sealcentre Pieterburen in The Netherlands admitted 3,775 seals for rehabilitation. Of these, 37 individuals presented clinical and radiologic signs of bone abnormalities indicative of osteomyelitis or infectious arthritis refractory to medical treatment. Seven cases resulted in euthanasia, and 30 cases underwent amputation surgery. The surgical procedure involved amputation of part of a flipper (24; two animals twice) or of a complete flipper (eight). All procedures were done under general anesthesia except one that was performed with local anesthesia, and all 30 animals were released. In two cases, the osteomyelitis presented with the rare Totenlade phenomenon, a sequestrum surrounded by new periosteal bone formation. The purpose of this retrospective study was to evaluate the outcome of the operative treatment of osteomyelitis and infectious arthritis in the flippers of harbor (Phoca vitulina) and grey seals (Halichoerus grypus) during this 6-yr period.