As part of the commissioning procedure of a linear accelerator at our cancer center, the defining laser lines were aligned with the optical and radiation isocenter of the linac. When a mechanical checkout jig was set up at the same point, a discrepancy of 4 mm resulted when the gantry was moved from 0 degrees to 180 degrees. Extensive measurements, some with custom-designed devices, confirmed the observations and provided an explanation. Even though the mechanical isocenter is within the specified tolerance of 1-mm radius, the clinically observable discrepancy of 4-mm results from the noncoincidence of the mechanical and radiation isocenters. The clinical significance of the final setup is discussed and future commissioning procedures are recommended.