The present study aimed to investigate the antiproliferative effect of embryonic stem cell-conditioned medium (ESC-CM) on the mouse liver cancer Hepa1-6 cells in vitro. Furthermore, in order to elucidate the underlying molecular mechanism, the microRNAs (miRNAs) in ESC-CM associated with the inhibition of Hepa1-6 proliferation were identified. Following the co-culture of ESC-CM and Hepa1-6 in Transwell chambers, the proliferation, cell cycle, apoptosis and associated protein expression were determined in Hepal-6 cells. Moreover, miRNA array analysis was employed to identify differentially expressed miRNAs. Based on the differentially expressed miRNAs, the target genes and potential associated signaling pathways were determined. Finally, RT-qPCR was conducted to confirm the above results. The ESC-CM inhibited Hepal-6 cell proliferation and increased the percentage of cells at G 1 phase and decreased the percentage of cells at the G 2 /M phase of the cell cycle. The expression of cyclin D1/cyclin-dependent kinase (CDK)4/CDK6 was decreased following co-culture, with no effect on cell apoptosis. Six significantly regulated miRNAs were identified and 423 putative target genes of these regulated miRNAs were predicted. Gene ontology analysis revealed the putative target genes to be associated with the 'DNA replication (GO: 0006260)' GO term, 'apoptosis' and 'signal transduction'. The Kyoto Encyclopedia of Genes and Genomes analysis indicated that deregulated miRNAs were enriched in the Wnt signaling (KEGG entry: Map 04310) and Hippo signaling pathways (KEGG entry: Map 04390), pathways associated with cancer. Overall, the present study demonstrated the inhibition of Hepa1-6 cell line proliferation upon treatment with ESC-CM, by decreasing cell cycle-associated protein cyclin D1/CDK4/CDK6 expression and arresting cells in G 1 phase of the cell cycle, with no effect on cell apoptosis. Furthermore, the inhibition of proliferation by ESC-CM may be mediated by miRNAs that affect cell cycle-associated mRNAs and the Wnt signaling pathway.