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Accurately calculating setup errors is crucial in ensuring quality assurance for patients undergoing radiation therapy treatment. This cross-sectional study aimed to determine the systematic, random, and planning target volume (PTV) margin errors for patients with head and neck cancer (n=48) and breast cancer (n=50). The treatment setup was performed using electronic portal imaging (EPIDs) and irradiated using Elekta linac. The errors were calculated using the van Herk formula. The systematic error for the head and neck was 0.89, 0.43, and 1.49 mm on the x, y, and z-axis, respectively, and 0.39, 0.74, 0.38 for the breast cases. The random error was 0.82, 0.68, 0.94 mm for the head and neck and 0.66, 0.72, 0.79 mm for the breast. The PTV margin shifting error for the head and neck were 2.79, 1.55, and 4.38 mm, while it was 1.43, 2.35, and 1.50 mm for the breast. The setup errors varied according to the tumor location. The study highlights the potential benefits of using EPIDs for reducing uncertainties in setup verification procedures.