Recent studies on dental morphology in mammals have explored the genetic basis of phenotypic variation through morphometric integration. However, reports on metameric shape variation in humans are scarce. This study focuses on the geometric shape and size of upper P4-M1 in individuals of three geographic dispersed populations from Africa (Hutu, n = 11), Asia (Javanese, n = 13) and America (Inuit, n = 9). The covariation patterns among teeth were analyzed to test their degree of modular integration. Shape and size variation was extracted from landmark configuration, located at occlusal surface on digital images, using generalized least-square Procrustes superimposition for each tooth. Two-block partial least-squares analysis and vector correlation (Rv) coefficient were used to quantify the total amount of cross-covariance between two subset of landmarks corresponding to each tooth. Results show higher levels of tooth-shape complexity compared with size. We found non-significant covariation between P4 and M1 shapes but covariation was found in size of the three analyzed populations (Rv > 0.7; P < 0.01). This suggests independent shape variation in these two tooth classes whereas their size is integrated. In addition, Procrustes distances derived from canonical variates analysis among groups show higher morphological differences between Asian (P < 0.001) and African–American (P = 0.011) populations. Our findings suggest that upper P4-M1 complex develop from different morphogenetic fields which affect shape but not size in human populations, and secondly, that dental morphometric difference among populations could result by non-random processes, such as phylogenetic and/or ecological factors.