Human immunodeficiency virus-1 (HIV-1) infection severely damages the gut-associated lymphoid tissue (GALT), the immune system and the gut barrier, which leads to accelerating the disease progression for patients with acquired immune deficiency syndrome (AIDS). Dysregulation of microRNAs (miRNAs) may contribute to this process. However, few studies have investigated the importance of miRNAs in AIDS pathogenesis and progression. The whole miRNA profile of patients with HIV infection from southwest P.R. China and the mode of interaction between HIV-1 and miRNAs remains to be elucidated. Colon mucosal samples were collected from HIV+ patients and HIV-healthy individuals, miRNAs were isolated and subjected to array hybridization in the present study. A total of 476 human and virus-derived microRNAs were significantly altered in the HIV+ group when compared with the control group (P< 0.05), which may be involved in the progression to AIDS. Target genes of the significantly altered miRNAs were predicted using the TargetScan, miRbase and miRanda databases and the 10 shared target genes of upregulated miRNAs and the 391 target genes of downregulated miRNAs were selected. As only 10 target genes were predicted for upregulated miRNAs, subsequent GO and KEGG pathway analyses were focused on the 391 target genes of the downregulated miRNAs. The findings of the present study identified a series of crucial pathways, including cell-extracellular matrix interaction and chemokine regulation, which indicated close affinity with CD4(+) T cell activation. These pathways, involving genes such as integrin alpha 5, led to a gut barrier dysfunction of patients with HIV. Important miRNAs include hsa-miRNA-32-5p, hsa-miRNA-195-5p, hsa-miRNA-20b-5p, hsa-miRNA-590-5p. The expression levels of the miRNAs and their target genes were confirmed using RT-qPCR. Taking into previous observations, the findings of the present study identified the importance of miRNAs for regulating gut barrier dysfunction via multiple regulatory molecules and signaling pathways, which elucidated the underlying molecular mechanism of gut barrier dysfunction in patients with HIV.