Over the past 10 years it has become evident that fatty acids regulate cellular functions by modulating gene expression. Fatty acids and fatty acid metabolites exert some of their effects on gene expression by affecting the activity of nuclear transcription factors, peroxisome proliferator-activated receptors and sterol regulatory element binding protein type 1. The present review describes the latest developments in the field, with particular emphasis on the physiological roles of the various peroxisome proliferator-activated receptor isotypes, including their implication in the control of proliferation and differentiation of normal and malignant cells, and on the mechanisms implicated in the regulation of sterol regulatory element binding protein type 1 activity by polyunsaturated fatty acids.