Size and shape changes in the skull of South American spiny rats Proechimys spp. were investigated using geometric morphometrics. Six species were studied (P. guairae, P. poliopus, P. trinitatis, P. canicollis, P. mincae and Proechimys sp.) using 12 populations from Venezuela and Colombia. Proechimys poliopus, P. guairae and Proechimys sp. have undergone recent speciation coupled with chromosomal rearrangements. The separate analysis of size and shape showed that the only sexually dimorphic character is size; P. mincae is the smallest species and Proechimys sp. the largest. The populations are all recognizable by their shape, and populations of the same species share a common kind of shape modification. The prevalent non-uniform nature of morphological change in the skull shows how the various structures, such as those involved with audition, feeding and olfaction, are modified differently among species. Consequently, the modification of these different structures over a long time could reflect a progressive diversification of the microniche of each species.