A method has been developed in order to digitally correlate ion and optical microscopic images of the same sample areas. Serial cross-sections of human thyroid tissue were analyzed by secondary ion mass microscopy and by light microscopy. The resulting chemical and immunochemical map images were superimposed and correlated by means of a two-pass registration algorithm which allows to correct for geometrical distortions introduced by the ion microscope. Results are presented for the study of thyroglobulin chemical modification in pathological thyroid tissue that demonstrates heterogeneous molecular activity