The goal of the study was to evaluate the inter- and intrafractional patient setup accuracy of target volumes located in the head, thoracic, abdominal, and pelvic regions when using SGRT, by comparing it with that of laser alignment using patient skin marks, and to calculate the corresponding setup margins. A total of 2303 radiotherapy fractions of 183 patients were analyzed. All patients received daily kilovoltage cone-beam computed tomography scans (kV-CBCT) for online verification. From November 2019 until September 2020, patient setup was performed using laser alignment with patient skin marks, and since October 2020, using SGRT. The setup accuracy was measured by the six degrees of freedom (6DOF) corrections based on the kV-CBCT. The corresponding setup margins were calculated using the van Herk formula. Analysis of variance (ANOVA) was used to evaluate the impact of multiple factors on the setup accuracy. The inter-fractional patient setup accuracy was significantly better using SGRT compared to laser alignment with skin marks. The mean three-dimensional vector of the translational setup deviation of tumors located in the thorax, abdomen, and pelvis using SGRT was 3.6 mm (95% confidence interval (CI) 3.3 mm to 3.9 mm) and 4.5 mm using laser alignment with skin marks (95% CI 3.9 mm to 5.2 mm; p = 0.001). Calculation of setup margins for the combined inter- and intra-fractional setup error revealed similar setup margins using SGRT and kV-CBCT once a week compared to laser alignment with skin marks and kV-CBCT every other day. Furthermore, comparable setup margins were found for open-face thermoplastic masks with AlignRT compared to closed-face thermoplastic masks with laser alignment and mask marks. SGRT opens the possibility to reduce the number of CBCTs while maintaining sufficient setup accuracy. The advantage is a reduction of imaging dose and overall treatment time. Open-face thermoplastic masks may be used instead of closed-face thermoplastic masks to increase the patient's comfort.