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Introduction: Reliability of foramen magnum dimensions using post-mortem computed tomography (PMCT) to obtain standardized measurements for biological profiling with interest in sexual dimorphism needs to be evaluated prior to a larger scale population-based study. Method: This was a retrospective cross-sectional study of 40 Malaysian adult decedent PMCT skulls. Standardized morphometric evaluation of two foramen magnum parameters, the foramen magnum anterior-posterior diameter (FMAPD) and transverse diameter (FMTD), were performed by three readers at two separate times. Statistical analysis included intraobserver and interobserver relative technical error of measurement (RTEM), coefficients of reliability (R), and t-test. Results: Error rates (RTEM) for FMAPD demonstrated intraobserver values of 3.65–3.84% (R = 0.73–0.75, substantial reliability) and interobserver values of 4.12–5.23% (R = 0.56–0.68, moderate to substantial reliability). Error rates (RTEM) for FMTD demonstrated intraobserver values between 4.52% and 5.00% (R = 0.57–0.70, moderate to substantial reliability) and interobserver values between 5.50% and 6.38% (R = 0.48–0.64, moderate to substantial reliability). Discussion: To improve precision of a population-based study, we recommend specialized operator training in the use of PMCT software, adequate sample size, clear landmark definitions, and consideration of population affinity as a confounder.