To date, there are more than two thousand human miRNAs, each of them may be involved in the regulation of hundreds of protein coding target genes. Methylation of CpG-islands, in turn, affects miRNAs gene expression. Our aim was to evaluate the role of methylation in the regulation of miRNA gene expression and, consequently, in the regulation of expression of target genes in primary lung tumors. Using a common collection of non-small cell lung cancer samples we performed a comprehensive study, including analysis of the methylation status and expression levels of some miRNA genes and their potential target genes on chromosome 3: RAR-beta2 and NKIRAS1. Increased frequency of methylation in lung tumors compared to histologically normal tissue was revealed for miR-9-1 and miR-34b/c genes with significant statistics (P < or = 0.05 by Fisher exact test) and for miR-9-3 and miR-193a was marginally significant (P < or = 0.1). Significant correlation was revealed between alterations of methylation and expression level of miR-9-1 gene (P = 5 x 10(-12) by Spearman) in the lung tumors, this suggests the role of methylation in the regulation of expression of this miRNA genes. Besides, a statistically significant negative correlation (P = 3 x 10(-12)-5 x 10(-13) by Spearman) was found between alterations of expression levels of miR-9-1 and miR-17and RAR-beta2 target gene and also between expression level alterations of miR-17 and NKIRAS1 that was not previously analyzed. The inverse relationship between expression levels of miRNA genes and their target genes is consistent with the known mechanism of suppression of protein coding genes expression under the action of miRNAs. For the first time significant correlations (P = 3 x 10(-10)-4 x 10(-13) by Spearman) were shown between alterations of methylation status of miRNA genes (miR-9-1, miR-9-3, miR-34b/c, miR-193a) and the expression level of RAR-beta2 target gene and between alterations of methylation status of miR-34b/c, and miR-193a and the expression level of NKIRAS1 target gene in the primary lung tumors, which suggests the possibility of indirect effects of methylation of miRNA genes on expression level of target genes.