Heterotaxia is a group of congenital disorders characterized by a misplacement of one or more organs according to the left-right axis. Bilateral asymmetry of internal organs is conserved among all vertebrate species. Analyses in animal models such as mouse, chicken, frog and zebrafish allowed for a remarkable progress of knowledge on the embryonic and genetic mechanisms underlying internal left-right asymmetry. In this review we focus on the insights from these model organisms that are useful for a better understanding of the etiology and pathogenesis of human heterotaxia. The known causes of human heterotaxia are reviewed and situated within the conceptual framework that originates from vertebrate model organisms. Furthermore, we attempt to apply the rapidly increasing insights gained from both animal models and human genetics to clinical practice in order to contribute to a more accurate conceptual classification, genetic diagnosis and counseling.