The normal human heart contains epicardial adipose tissue (EAT) and myocardial fat. The associations between obesity, myocardial fat, visceral adipose tissue (VAT), and cardiovascular disease are not fully understood. The objective of this study was to estimate myocardial fat using stereological methods and investigate its relations with obesity, EAT, and VAT. To establish the EAT volume, 115 deceased individuals were included, and postmortem computed tomography was conducted on their eviscerated hearts. Six samples from the left and right ventricles (LV and RV) of the heart were stereologically examined to calculate the percentage of myocardial fat. Kidney and omental fat were weighed at autopsy, and the waist–hip ratio was calculated. Females had a slightly non-significantly (p = 0.054) larger proportion of RV fat (13.2% ± 4.4) compared to that in men (11.5% ± 2.7). We found a significant positive correlation between body mass index (BMI) and LV myocardial fat (p = 0.033). In the RV, this correlation was only at the borderline of significance (p = 0.052). The EAT volume was positively correlated with both RV and LV myocardial fat. We found no association with the waist–hip ratio (WHR) or the omental or kidney fat as measures of VAT. The myocardial fat was normal, most prominent in the RV, and correlated with the EAT and, partly, BMI. We found no association with VAT.