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Micro-RNAs (miRNAs) are small non-coding RNA molecules which provide a subtle layer of regulation to thousands of cellular genes. The identification of virally encoded miRNAs added another layer of complexity to the dense interaction between viruses and their natural hosts. While it has been shown that viral miRNAs can regulate both cellular and viral gene expression, target identification has been a difficult and cumbersome task. The immunoprecipitation of Argonaute (Ago)-protein containing RNA-induced silencing complexes (RISC) followed by microarray analysis (RIP-Chip) allows the identification of miRNA-targetomes at whole transcriptome level. We applied Ago2-based RIP-Chip to identify cellular transcripts targeted by Kaposi's sarcoma-associated herpesvirus (KSHV, n=114), Epstein-Barr virus (EBV, n=44) and cellular miRNAs (n=2,337) in six latently infected or stably transduced human B-cell lines. While RIP-Chip yields a plethora of high-confidence miRNA targets and provides a quantitative estimate of miRNA function, additional biochemical methods like HITS-CLIP or PAR-CLIP and bioinformatic analysis are required to identify individual miRNA binding sites. Together, these methods will be useful to unravel the network of regulation exerted by both viral and cellular miRNAs, thereby providing the basis for functional studies on miRNA-mediated regulation of gene expression in herpesvirus infections.