Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors belonging to the nuclear receptor superfamily. Three PPARs isoforms have been characterized: PPARα, β/δ and γ. As other nuclear receptors, the PPARs are organized in distinct functional domains: A/B, C or DNA binding domain (DBD), D, E or ligand binding domain (LBD) and F. The A/B domain contains the activation function 1 (AF-1) which is transcriptionally active in absence of ligands. The DBD and the LBD of the PPARs determine the specificity of promoter DNA sequence recognition and ligand recognition, respectively. An activation function 2 (AF-2) is contained in the E domain, which mediates the ligand-dependent activation of the receptor. The transcriptional activity of the PPARs is regulated by post-translational modifications, such as phosphorylation and ubiquitination. Phosphorylation of PPARs is controlled by environmental factors activating different kinase pathways leading to the modulation of their activities. PPARs degradation by the ubiquitin–proteasome system modulates the intensity of the ligand response by controlling the level of PPAR proteins in the cells. PPARs also control the expression of genes implicated in the inflammatory response via negative interference with different inflammatory pathways, such as NFκB, AP-1, C/EBP β, STAT-1 and NFAT. As such, PPARs influence inflammatory cytokine production and cell recruitment to the inflammatory sites. A better understanding of the mechanism of action of PPARs could improve the design of more specific and more efficient novel drugs. Molecules with dissociated effects could be useful for the treatment of lipid disorders or inflammation.