MicroRNAs (miRNAs) are a class of small noncoding RNAs involved in posttranscriptional regulation. miRNAs are utilized in organisms ranging from plants to higher mammals, and data have shown that DNA viruses also use this method for host and viral gene regulation. Here, we report the sequencing of the small RNAs in rat cytomegalovirus (RCMV)-infected fibroblasts and persistently infected salivary glands. We identified 24 unique miRNAs that mapped to hairpin structures found within the viral genome. While most miRNAs were detected in both samples, four were detected exclusively in the infected fibroblasts and two were specific for the infected salivary glands. The RCMV miRNAs are distributed across the viral genome on both the positive and negative strands, with clusters of miRNAs at a number of locations, including near viral genes r1 and r111. The RCMV miRNAs have a genomic positional orientation similar to that of the miRNAs described for mouse cytomegalovirus, but they do not share any substantial sequence conservation. Similar to other reported miRNAs, the RCMV miRNAs had considerable variation at their 3 and 5 ends. Interestingly, we found a number of specific examples of differential isoform usage between the fibroblast and salivary gland samples. We determined by real-time PCR that expression of the RCMV miRNA miR-r111.1-2 is highly expressed in the salivary glands and that miR-R87-1 is expressed in most tissues during the acute infection phase. Our study identified the miRNAs expressed by RCMV in vitro and in vivo and demonstrated that expression is tissue specific and associated with a stage of viral infection.MicroRNAs (miRNAs) are small noncoding RNAs involved in posttranscriptional regulation through binding to complementary sequences in target mRNAs resulting in gene silencing (4). miRNAs are ubiquitous among multicellular eukaryotic organisms, including plants and higher mammals, and have diverse roles in many different biological processes, including development, differentiation, proliferation, apoptosis, and hematopoiesis (35,51). In addition to eukaryotic miRNAs, DNA viruses, mainly of the Herpesvirus family, have been shown to encode miRNAs. Bioinformatic, sequencing, and direct cloning approaches have led to the identification of more than 140 viral miRNAs (reviewed in reference 55). The role of viral miRNAs is proposed to include the targeting of cellular genes to induce a favorable replication environment or to evade the host immune system and the targeting of their own viral genome to regulate viral gene expression during persistence or latency/reactivation (22, 55).Human cytomegalovirus (HCMV) is known to encode at least 14 miRNAs. HCMV is a ubiquitous betaherpesvirus, and primary infection results in lifelong persistent/latent infection of the host. Infection of immunocompetent hosts is generally asymptomatic, but infection of immunocompromised hosts can lead to high morbidity and mortality. HCMV has been linked to the development of atherosclerosis, arterial restenosis following angiopla...