We have developed and validated in a phantom a method of computer-assisted coregistration using multislice SPECT and MR images. Reusable fiducial markers were fabricated from nylon-based plastic and consist of two parts: a base that remains fixed to the skin with adhesive between scans and a removable, spherical cavity insert that can be filled with contrast agents appropriate for multiple imaging modalities. Markers external and internal to a three-dimensional brain phantom provided a means of quantifying the method's accuracy. A computer algorithm was used to derive transformation matrices for image sets by minimizing the root mean squared deviations obtained for multiple permutations (n = 10) of increasing numbers (range 3–11) of external SPECT/MRI point pairs. As defined by the average SEM mean residual deviations of noncoregistered internal fiducials, the minimal accuracy was 2.4 ± 0.3 mm (no marker > 3.6 mm) for three coregistration points and did not improve beyond seven to eight fiducials (2.2 ± 0.1 mm; no marker > 3.2 mm). The method's true accuracy is likely to be better than estimates of minimal accuracy, however, since such measures reflect surmountable random errors in fiducial location. With use of identical MRI (or SPECT) data sets, measures of intraoperator (0.5 ± 0.1 and 0.5 ± 0.1 mm, respectively) and interoperator (0.5 ± 0.3 and 0.8 ± 0.1 mm) reliability were also obtained, establishing the method as highly reproducible and objective. Preliminary results in a human subject suggest its feasibility for clinical studies.