Globally, the increasing need to conduct both research and surveillance of the health of wild animal populations has been recognized as an important tool in conservation and management. While such studies on terrestrial wildlife are frequent in the southern African sub-region, their counterparts in the marine environment seem to be largely lacking. Here we report on our experience in establishing and testing a standardized necropsy protocol for small cetaceans adapted for the local context, with the specific aim of sampling for health investigations and monitoring. The necessity, challenge and value of regional standardization in data collection specifically aimed at health investigations, inter-disciplinary collaboration, long-term data banking, and sample storage are discussed in addition to practical and safety considerations. The developed protocol, focusing on the necropsy technique and tissue sample collection, as well as a list of required equipment are available as .