The anti-apoptotic genes DAD-1 and HAX-1 and the pro-apoptotic GZMB gene have a significant role in the regulation of apoptosis in heart tissue. However, investigation into these genes and their proteins in the pathogenesis of cardiovascular diseases remains limited. The aim was to characterize the association between the presence and distribution of pro-apoptotic and anti-apoptotic genes and their proteins in the right atrial appendage affected by coronary heart disease (CHD) and aortic valve stenosis (AoS) and to compare the findings with those of the control group. Tissue was obtained from the right atrial appendage of 15 patients with CHD and AoS during elective open-heart surgeries. Control samples were collected from 5 pediatric individuals from archival material held in the historical anatomy collection. Tissue samples were stained with H&E for routine examination. The HAX-1 and GZMB proteins were detected by immunohistochemistry, while CISH was used to identify HAX-1, GZMB, and DAD-1 genes. The results were evaluated semi-quantitatively and analyzed using the Mann-Whitney U test and Spearman's correlation coefficient. The patients exhibited a moderate number of cardiomyocytes positive for HAX-1 and GZMB proteins, while controls displayed numerous to abundant positive cells. The DAD-1 gene was equally expressed in controls and patients, while HAX-1 and GZMB-positive cells were predominant in the control tissue. A statistically significant difference in positive HAX-1 gene cardiomyocytes was observed between the patients and controls only. A positive correlation was detected between the expression of the HAX-1 gene and the corresponding HAX-1 protein. The decreased expression of the HAX-1 gene and a tendency toward reduced GZMB gene expression in patient tissue may reflect, at least in part, an apparent balance in apoptosis-related expression patterns associated with GZMB and HAX-1 in cases of CHD and AoS, with potential contributions from age- and disease-related differences. The use of both CISH and IHC analyses provided complementary assessment of the observed findings. Additionally, no differences were found in DAD-1 gene expression between control and CHD/AoS-affected cardiomyocytes, which may reflect a less prominent or variable role of this gene in the studied conditions.