microRNAs are important regulators of gene expression that guide translational repression and degradation of target mRNAs. Only relatively few miRNA targets have been characterized, and computational prediction is hampered by the relatively small number of nucleotides that seem to be involved in target recognition. Argonaute (Ago) crosslinking and immunoprecipitation (CLIP) in combination with next-generation sequencing proved to be a successful method for identifying targets of endogenous cellular miRNAs on a transcriptome-wide scale. Here we review various approaches to Ago CLIP, describe in detail the PAR-CLIP method and provide an outline of the necessary computational analysis for identification of in vivo miRNA binding sites.