RNA-binding proteins (RBPs) function importantly in RNA synthesis and metabolism by interacting with specific RNAs. The identification of RNA-protein interactions is required for understanding the cellular function mechanisms. A new technique, PAR-CLIP (photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation), has been used to determine the target transcripts of a few RBPs and map the RNA binding sites in a genome-wide fashion. In this study, a rapid and effective method was developed on the basis of PAR-CLIP to detect the RNA binding activity of putative RBPs and their complexes, termed UV cross-linking and tandem affinity purification (CLiTAP). The improvements include: (1) Tandem affinity purification was performed to purify RNA-protein complexes efficiently; (2) Sypro Ruby staining and autoradiography were used sequentially to determine which protein(s) possessing RNA-binding activities. CLiTAP was used to analyze the RNA binding activity of three kinds of CCCH-type zinc finger proteins, TbZC3H7, TbZC3H34 and TbZC3H5, in Trypanosoma brucei. TbZC3H7, a core component of RNA cap-binding complex, showed a strong RNA-binding ability. TbZC3H34, a hypothetical protein, displayed a weak RNA-binding activity, while one of its interacting proteins showed a strong activity. In contrast, TbZC3H5 and all its interacting proteins did not show any RNA binding activity. These results indicated that CLiTAP is an efficient method and can be used to experimentally identify the RBPs in a protein complex, which provide a basis for further mapping the RNA binding sites and investigating the structure and mechanism of RBPs.