Background: Relatively little is known about the genetic architecture of childhood behavioral disorders in very young children. Method: In this study, parents completed the Infant-Toddler Social and Emotional Assessment, a questionnaire that assesses symptoms of childhood disorders, as well as socio-emotional competencies, for 822 twin pairs (49.3% female; age 17-48 months) participating in the Wisconsin Twin Project. Psychometric, rater bias, and sex-limitation models explored the role of genetic and environmental influences on (1) externalizing and internalizing behavior; (2) less commonly assessed behaviors pertaining to physical and emotional dysregulation, general competencies, social relatedness; and (3) infrequent behaviors such as those associated with pervasive developmental delays. Results: Heritable influences accounted for the majority (56% or more) of variation in behavior that was commonly observed by both parents. The remaining variance was associated with non-shared environmental factors, with the exception of competency and atypical behavior, which were also influenced by shared environmental factors. In contrast, for most behaviors, the variation unique to mother and father ratings was split between variation due to shared environment or rater biases and to measurement error. Little evidence emerged for sex differences in the underlying causes of variation.