PURPOSE We investigated aligning a transmission (T) scan with a subsequent emission contaminated transmission (T+E) scan. This would permit correction for patient motion and thereby use of a single T scan to correct E scans taken hours or days apart. METHOD Scans from 15 patients were used to produce 200 T scans contaminated with two levels of either [18F]fluorodeoxyglucose or [13N]ammonia E data. Known misalignments were introduced between each T+E scan and the corresponding T scan, and each pair was subsequently realigned. Realignment errors were compared with those obtained for uncontaminated T scans. RESULTS The realignment errors increase with the contamination level and depend slightly on the contaminant. However, even at the highest level of contamination studied, the mean absolute translation errors remained less than the voxel size and the mean absolute rotation errors were < 2.5 degrees. CONCLUSION AT+E scan can be accurately realigned with a T scan. This suggests that attenuation correction could be performed by using a high quality T scan taken days or hours earlier and aligning this T scan with a short T scan taken immediately after E imaging.