Histone modifications contribute to the precise regulation of transcription by recruiting non-histone proteins and controlling chromatin conformation. These covalent modifications are dynamically regulated by many enzymes that modify histones at specific residues in different ways. Histone modifiers contribute to development as well as cellular responses to extracellular stimuli. Mutations in the genes encoding them cause various diseases, including developmental disorders and certain malignancies. Haploinsufficiency for some histone methyltransferases, one of the principal modifiers of the histone modification network, are associated with particular congenital diseases, including Sotos syndrome, Wolf-Hirschhorn syndrome, and 9q syndrome. In this review, we discuss the molecular function of the histone methyltransferases and the human diseases associated with their dysfunction.