Congenital limb malformations exhibit a wide spectrum of phenotypic manifestations and may occur as an isolated malformation and as part of a syndrome. They are individually rare, but due to their overall frequency and severity they are of clinical relevance. In recent years, increasing knowledge of the molecular basis of embryonic development has significantly enhanced our understanding of congenital limb malformations. In addition, genetic studies have revealed the molecular basis of an increasing number of conditions with primary or secondary limb involvement. The molecular findings have led to a regrouping of malformations in genetic terms. However, the establishment of precise genotype-phenotype correlations for limb malformations is difficult due to the high degree of phenotypic variability. We present an overview of congenital limb malformations based on an anatomic and genetic concept reflecting recent molecular and developmental insights.