Rapid developments in the elucidation of simple Mendelian traits in humans, the complexity of genotype–phenotype relationships, and the growing appreciation of complex genetic traits have conspired to focus interest on the role of modifier genes in humans. This paper reviews categories of genetic modifiers and their effects and then discusses non-Mendelian inheritance patterns involving modifier genes. Although genetic models from many disease classes of human and model systems will be considered, we focus this review on the implications for the understanding of pleiotropic malformation syndromes. Genetic modifiers have so far been molecularly defined in relatively few malformation syndromes, but the rapid acknowledgement of their critical role in human development is an exciting advance in contemporary attempts to understand the relationship of phenotype and genotype.