A procedure for patient repositioning and compensation for misalignment between transmission and emission data in positron emission tomography (PET) heart studies has been developed. Following the transmission scan (TR1), patients are moved from the scanner bed for the administration of the tracer, and repositioned when ready for the emission scan (EM1). A short postinjection transmission scan (TR2) is performed at the end of the EM1 study. TR1 and TR2 images are compared to recognize misalignment between transmission and emission studies. TR1 sinograms are compensated for misalignment to allow for a proper attenuation correction. The procedure has been tested on phantom and [18F]FDG PET heart studies. Misalignments down to 2.5 mm translation and 1 degree rotation in the transaxial plane and 4 mm in the axial direction can be recognized and compensated for. The procedure is suitable for clinical purposes, allowing reduction of patient time on the scanner bed, increased patient comfort and significant increase of patient throughput.