It is unclear what neural processes induce individual differences in perceptual organization in different modalities. To examine this issue, the present study used different forms of bistable perception: auditory streaming, verbal transformations, visual plaids, and reversible figures. We performed factor analyses on the number of perceptual switches in the tasks. A 3-factor model provided a better fit to the data than the other possible models. These factors, namely the "auditory," "shape," and "motion" factors, were separable but correlated with each other. We compared the number of perceptual switches among genotype groups to identify the effects of neurotransmitter functions on the factors. We focused on polymorphisms of catechol-O-methyltransferase (COMT) Val(158)Met and serotonin 2A receptor (HTR2A) -1438G/A genes, which are involved in the modulation of dopamine and serotonin, respectively. The number of perceptual switches in auditory streaming and verbal transformations differed among COMT genotype groups, whereas that in reversible figures differed among HTR2A genotype groups. The results indicate that the auditory and shape factors reflect the functions of the dopamine and serotonin systems, respectively. Our findings suggest that the formation and selection of percepts involve neural processes in cortical and subcortical areas.