Emerging evidence indicates that microRNAs (miRNAs) are often dysregulated and play a fundamental role in hepatocellular carcinoma (HCC). However, the mechanism underlying miRNA dysregulation is still elusive. In the present study, we adopted an integrated analysis strategy combining data from genome-wide methylated DNA immunoprecipitation chip and miRNA expression microarray to study the regulation of DNA methylation on miRNA expression in HCC. We first characterized 864 differentially methylated regions (DMRs) located in 236 miRNA regions between cancerous and normal hepatocytes in HCC. We observed that the occurrence of miRNA DNA hypomethylation was more common than its hypermethylation while miRNA DNA hypermethylation was usually found in CpG islands. Then through correlation analysis between miRNA methylation and expression data, we identified 10 dysregulated miRNAs under the potential regulation of DNA methylation in HCC. Five of them (miR-148a, miR-375, miR-195, miR-497 and miR-378) were in hypermethylation and down-regulation status, while another five (miR-106b, miR-25, miR-93, miR-23a and miR-27a) were in hypomethylation and up-regulation status in HCC. Bioinformatics analysis showed that miR-148a may form a negative feedback loop with its targets DNMT1 and DNMT3B and the expression of the miR-195/497 cluster may be affected not only by their hypermethylated promoter region but also by their hypermethylated transcription factors NEUROG2 and DDIT3. Conclusion: our preliminary data and bioinformatics analysis suggest that DNA methylation plays an important and complex role in the regulation of miRNA expression in HCC, which may provide insights into the pathogenesis of HCC and thus may be used for diagnosis and intervention.