In order to understand the mechanisms by which RNA-binding proteins carry out their functions, it is important to identify where they bind their targets. To facilitate this, the UV-crosslinking and Immunoprecipitation (CLIP) method was developed which allows for in vivo identification of protein-RNA interactions. To identify the sequence of CLIP RNAs, these need to be ligated to adapters and amplified to a cDNA library, which can be an inefficient process that had been improved over the last years. In this chapter, we present the general CLIP protocol and describe how the individual steps in the protocol can be optimized depending on the protein studied and the cell type or tissue used. © 2012 Wiley-VCH Verlag GmbH & Co. KGaA.