Myocardial SPECT/CT imaging is frequently performed to assess myocardial perfusion and dynamic parameters of heart function, such as ejection fraction (EF). However, potential pitfalls exist in the imaging chain that can unfavorably affect diagnosis and treatment. We performed a national cardiac quality control study to investigate how much SPECT/CT protocols vary between different nuclear medicine units in Finland, and how this may affect the heart perfusion and EF values. Altogether, 21 nuclear medicine units participated with 27 traditional SPECT/CT systems and two cardiac-centered IQ-SPECT systems. The reproducibility of EF and the uniformity of perfusion were studied using a commercial dynamic heart phantom. SPECT/CT acquisitions were performed and processed at each participating unit using their own clinical protocol and with a standardized protocol. The effects of acquisition protocols and analysis routines on EF estimates and uniformity of perfusion were studied. Considerable variation in EF estimates and in the uniformity of perfusion were observed between the units. Uniformity of perfusion was improved in some units after applying the higher count-statistic standard acquisition protocol. EF estimates varied more due to differences in analysis routines than as a result of different acquisition protocols. The results obtained with the two IQ-SPECT systems differed substantially from the traditional multipurpose cameras. On average, the EF and heart perfusion were accurately estimated by SPECT/CT, but high errors could be produced if the acquisition and analysis routines were poorly optimized. Eight of the 21 participants altered their imaging protocol after this quality control tour.