Neurobiological research in alcohol dependence has led to a new understanding of this addictive disease. While some important mechanisms like alterations in the mesolimbic reward system or changes in the hypothalamus-pituitary-adrenocortical axis have been well studied, other possible neurobiological mechanisms are still unrevealed. This applies for the role of specific neuroendocrinological pathways like the appetite-regulating system and the modification of gene expression, particularly the influence of genetic variants of transcription factors or epigenetic mechanism like DNA methylation or histone acetylation. This review describes the current knowledge regarding these factors, focusing particularly on the role of appetite- and volume-regulating hormones, the role of genetic variants of specific transcription factors and the function of epigenetic alterations in the genomic sequence of candidate genes for alcohol dependence. A further understanding of the influence of transcription factors and epigenetic regulation may help to elucidate the pathophysiological mechanisms in the neurobiology of alcohol dependence.