The peroxisome-proliferator activated receptors (PPARs) are members of the nuclear receptor family. They are involved in the development of a number of diseases such as type 2 diabetes, dyslipidemia, and cancer.As such, PPARs are important targets for drug development necessitated a detailed understanding of the interaction between PPARs and their protein binding partners. During the last 15 years, chemical cross-linking combined with mass spectrometry has evolved into an alternative tool to obtain structural information of a protein or protein complex. Aim of this work was to obtain three-dimensional structural information of PPAR-α and -β/δ upon ligand binding by chemical cross-linking and by specifically incorporating photoreactive amino acids. Therefore, conformational changes upon ligand binding as well as additional data of the highly flexible N-terminus of PPAR-β/δwere elucidated.