Background and aim: Obesity is associated with an increase in different adipose depots. The anatomic distribution of internal adipose confers different risks. Recently, significant interest has emerged in the expansion of epicardial adipose tissue (EAT) as a mediator of adverse cardiovascular events. Often, post-mortem examination remains the best method of investigating morphological changes in health and disease. This study aimed to develop a simple, reproducible, and non-invasive protocol for the measurement of internal adiposity using post-mortem computed tomography (PMCT). Patients and methods: 101 consecutive post-mortem subjects underwent non-contrast computed tomography scans. Measurements were performed using the open-source software 3D Slicer by a non-expert researcher. An expert radiologist and cardiologist verified the abdominal and cardiac sites of adiposity, respectively. We aimed to develop a protocol to measure total EAT, sub-depots of EAT, extra-pericardial adipose, visceral and subcutaneous adipose, and suprasternal adipose. Results: We found excellent reproducibility for our measures of total EAT, anterior right atrial EAT, extra-pericardial adipose, and visceral adipose tissue, with intraclass correlations between 0.82 and 0.99 for each measure. Due to a lack of suitable anatomical boundaries, other sub-depots of EAT, including in the interventricular groove, were not reproducible. Conclusions: Quantification of total EAT and anterior right atrial EAT are readily reproducible using 3D Slicer on post-mortem CT. They can be reliably measured by non-expert researchers with a small amount of training, and therefore be used to investigate morphological changes in adiposity in health and disease.