Fatty acids are known to serve as energetic substrates, key components of membrane lipids, and as substrates for the synthesis of signaling molecules and complex lipids. They are also known to be ligands either of membrane receptors involved in cell signaling or of nuclear receptors mediating gene regulation. Accumulation of fatty acids due to altered metabolism and/or unbalanced diet has been described to be toxic for several tissues, especially liver. In numerous cell types, cell death, cytokine secretion and activation of inflammatory processes appear to be a consequence of fatty acid accumulation. This review presents the different classes of fatty acids known to trigger toxic effects and inflammation, the cellular and subcellular targets of these fatty acids in the context of non-alcoholic fatty liver disease (NAFLD), and the mechanisms by which these effects are mediated.