With the increasing importance of posttranscriptional regulation, in particular translational regulation in development and disease, researchers are developing a methodology to dissect the interactions between RNA binding proteins and their RNA targets. One key aspect of this investigation is identifying RNA targets of those RNA-binding proteins using the UV-cross-linking immunoprecipitation approach. Such a crosslinking immunoprecipitation (CLIP) methodology is potent in identifying targets of RNA-binding proteins in many cell lines. An extension of such a technology is to apply the CLIP approach to tissue and organs to reveal RNA targets of physiological relevance. Here, we summarize our methods in identifying RNA targets from mouse testes and fly testes by enhanced CLIP (eCLIP) method and propose this eCLIP method could be applied to testes of most animal species if an effective antibody is available to an RNA binding protein of interest.