Transcription factors are highly conserved proteins with preserved structure and function for up to a hundred million years. They regulate protein formation and function by binding to DNA and controlling gene expression. Mutations are generally lethal, but can play role in endocrine disorders and tumor genesis. They are necessary for cell growth, proliferation, differentiation and are required in tissue and organ development during normal embryogenesis. Consequently, transcription factors are essential in developmental processes and homeostasis. Mutations of genes encoding transcriptional regulators have been shown to be involved in a number of various genetic diseases, in particular malformation of the skeletal system, cranium, limbs, as well as some congenital syndromes with anomalies of these organs and somatic/mental retardation. Evidences accumulate to support the need of transcription factor mutation identification in the clinical practice. The present study reviews the most important congenital malformations and genetic syndromes which are thought to be related to mutations in classic transcription factors, and in which determination of transcription factors might be of clinical significance, even in the near future, for exact causative diagnosis and genetic counseling in affected families. In addition, studies of the transcription factors may lead to a better understanding of human embryogenesis.