Epstein-Barr virus (EBV)-encoded small non-coding RNAs (EBERs) are abundantly expressed in various EBV-associated malignancies, and play critical roles in cell proliferation, tumorigenesis, and apoptosis resistance. However, the mechanism how EBERs regulate cell function awaits further clarification. In this study, we investigated the effect of EBERs on the expression of cellular microRNA (miRNA) and mRNA expression. To test the effect of EBERs while unaffected by other EBV genes, we used EBERs-deleted recombinant EBV infected Burkitt's lymphoma cell line (Akata(+)EBERs(-)) as well as EBV-infected (Akata(+)) and EBV uninfected (Akata(-)) cell lines. They all have the same genetic backgrounds. First, 15 different cellular miRNAs which have reverse complementary sequences to EBERs and have reported targets were selected by bioinformatics analysis. When RT-PCR was carried out for the 16 miRNAs using RNAs from Akata(+), Akata(-), and Akata(+)EBERs(-) cells, hsa-miR-7-5p was the only one showing down-regulated expression in Akata(+) than in Akata(-) and Akata(+)EBERs(-) cells. Bioinformatics and mRNA microarray analyses for Akata(+), Akata(-), and Akata(+)EBERs(-) cell lines were then carried out to predict putative targets of hsa-miR-7-5p. Among the 6 predicted targets of hsa-miR-7-5p, only low density lipoprotein receptor-related protein 6 (LRP6) was up-regulated in EBERs-expressing cells when tested by RT-PCR and Western blot. However, luciferase reporter assay showed that the 3'-UTR of LRP6 was not directly targeted by hsa-miR-7-5p. Our data suggest that both hsa-miR-7-5p and LRP6 are regulated by EBERs in Akata cells, and these genes may partly mediate the tumorigenic function of EBERs in Burkitt's lymphoma.