The past decade has seen remarkable advances in defining the molecular mechanisms underlying formation of the embryonic left right (LR) axis. This information is slowly transforming our understanding of human birth defects that are caused by disturbed LR axis patterning. Reversals, isomerisms, or segmental discordances of thoraco-abdominal organ position, that is, classic heterotaxy, clearly indicate embryonic disruption of normal LR patterning. Other isolated birth defects, particularly cardiovascular malformations, may be caused by deficiencies in the same pathways. Here, we review the distinctive clinical features of human heterotaxias and try to summarize the known connections between them and the corresponding developmental pathways.