Although behavioral lateralization is known to correlate with certain aspects of brain asymmetry in primates, there are limited data concerning hemispheric biases in the microstructure of the neocortex. In the present study, we investigated whether there is asymmetry in synaptophysin-immunoreactive puncta density and protein expression levels in the region of hand representation of the primary motor cortex in chimpanzees (Pan troglodytes). Synaptophysin is a presynaptic vesicle-associated protein found in nearly all synapses of the central nervous system. We also tested whether there is a relationship between hand preference on a coordinated bimanual task and the interhemispheric distribution of synaptophysin as measured by both stereologic counts of immunoreactive puncta and by Western blotting. Our results demonstrated that synaptophysin-immunoreactive puncta density is not asymmetric at the population level, whereas synaptophysin protein expression levels are significantly higher in the right hemisphere. Handedness was correlated with interindividual variation in synaptophysin-immunoreactive puncta density. As a group, left-handed and ambidextrous chimpanzees showed a rightward bias in puncta density. In contrast, puncta densities were symmetrical in right-handed chimpanzees. These findings support the conclusion that synapse asymmetry is modulated by lateralization of skilled motor behavior in chimpanzees.