HIV replication and the cellular miRNA machinery interconnect at several post-transcriptional levels. To understand their regulatory role in the intestine, a major site of HIV/SIV replication, dissemination and CD4+ T cell depletion we profiled miRNA expression in colon following SIV infection (10-Acute-SIV, 5-uninfected). Nine (4-up and 5-down) miRNAs showed statistically significant differential expression. Most notably, miR-190b expression showed high statistical significance (Adjusted p=0.0032), the greatest fold change and was markedly elevated in colon and jejunum throughout SIV infection. Additionally, miR-190b upregulation was detected before peak viral replication and the nadir of CD4+ T cell depletion predominantly in lamina propria leukocytes. Interestingly non-SIV-infected macaques with diarrhea and colitis failed to upregulate miR-190b suggesting that its upregulation was neither inflammation nor immune-activation driven. SIV infection of in vitro cultured CD4+ T cells and primary intestinal macrophages conclusively identified miR-190b upregulation to be driven in response to viral replication. Further miR-190b expression levels in colon and jejunum positively correlated with tissue viral loads. In contrast, mRNA expression of MTMR6, a negative regulator of CD4+ T cell activation/proliferation significantly decreased in SIV-infected macrophages. Luciferase reporter assays confirmed MTMR6 as a direct miR-190b target. This first report describing dysregulated miRNA expression in the intestine identifies a potentially significant role for miR-190b in HIV/SIV pathogenesis. More importantly, miR-190b mediated MTMR6 downregulation suggests an important mechanism that could keep infected cells in an activated state thereby promoting viral replication. In future, the mechanisms driving miR-190b upregulation including other cellular processes it regulates in SIV-infected cells needs determination.