Certain NCI protocol patients are imaged repetitively over the course of many days or weeks. For several reasons, it is desired to be able to (l) align the images from one imaging session to another and (2) align the 2D nuclear medicine projection images with CT images of the same subject. Alignment of projection images from one imaging session to another permits more accurate quantitation of changes in uptake over time. Aligning scans done on subsequent days, also permits a single transmission scan to be used to perform absolute quantitation. Alignment of the nuclear medicine projection images with the CT data permits correlation of radiopharmaceutical uptake with morphological structure. In addition, the CT data may themselves be used to perform attenuation correction of the emission data. An investigation of alignment scheme (l) has been performed, using an adaptation of a technique previously published by our group for 3D alignment of PET data. The method was modified for alignment of 2D projection images, and uses maximal pixel to pixel correlation techniques, applied to the transmission scan. The method assumes lung borders are within the imaging field, and uses them to optimize the alignment. The method has now been thoroughly tested on phantoms and with simulated and actual motion of patient data. In addition, a program has been written to allow the physician to point to a region of interest on the emission data, and automatically display the corresponding CT slice. The CT alignment was accomplished by projecting the CT data into 2D and using the same alignment methodology. Future work will focus on alignment techniques in 3D SPECT, using emission data.