Handedness is the single most studied aspect of human brain asymmetries. For long it has been thought to be a monogenic trait that can produce an asymmetrical shift of cerebral mechanisms, thereby producing right handedness. Nevertheless, a single gene explaining a sufficient amount of phenotypic variance has not been identified. The results of several recent studies using advanced molecular genetic techniques suggest that a multifactorial model taking into account both multiple genetic and environmental factors, as well as their interactions, might be better suited to explain the complex processes underlying the ontogenesis of handedness. In this article, we review the new insights into handedness genetics provided by these studies and discuss, how integrating results from genetic and neuroscientific studies might help us to generate more accurate models of the ontogenesis of handedness. Based on these thoughts, we suggest several candidate gene groups (e.g. genes involved in the formation of the corpus callosum, asymmetrically expressed genes or genes involved in the development of structural left-right asymmetries) whose investigation would help to further understand the complex relation of genes, the brain and handedness.