Hepatocellular carcinoma has a high mortality rate, thus, there is a need for improvement of prognosis of such patients. The aim of the present study was to identify differentially expressed mRNAs and miRNAs between hepatocellular carcinoma tissues and their matched adjacent normal liver tissues, and to carry out a bioinformatics analysis. Agilent 8x60K microarray technology was used to detect the changes of mRNA and miRNA expression between hepatocellular carcinoma tissues and their matched adjacent normal liver tissues. To select differentially expressed mRNAs and miRNAs, gene ontology (GO) and pathway analysis were performed using bioinformatics methods. qPCR was used to verify the microarray data. As a result, 924 mRNAs and 21 miRNAs exhibited a higher expression in the hepatocellular carcinoma tissue than their matched adjacent normal liver tissue. In comparison with the adjacent normal tissue, the carcinoma tissue showed a downregulated expression of 1,770 mRNAs and 12 miRNAs. The GO and pathway analysis showed that these RNAs were involved in the transcription process, REDOX, signal transduction, ion transport, immune response, cell adhesion and binding functions. A total of 572 target genes of 14 miRNAs were identified, most of which were involved in tumors. The results of qPCR were in concordance with the microarray results. In summary, the differentially expressed mRNAs and miRNAs that include signal transduction, immune response and many other key links may provide novel targets for early diagnosis and therapy of hepatocellular carcinoma.