Background A keratocystic odontogenic tumor (KCOT) is a benign destructive recurrent odontogenic cystic neoplasm. The microRNAs (miRNAs) miR-15a and miR-16-1 function as negative regulators of the anti-apoptotic gene BCL2 at the post-transcriptional level. Notably, high Bcl-2 immunoexpression is found in the epithelial lining of KCOTs, while the loss of Bcl-2 immunopositive cells is observed in marsupialized cysts. The purpose of this study was to investigate whether the transcription of miR-15a and miR-16-1 is altered in KCOTs and whether it is associated with BCL2 gene expression in such lesions. Methods Using qRT-PCR and immunohistochemical analyses, we examined miR-15a/16-1 and BCL2 gene expression in KCOTs. The impact of miR-15a/16-1 expression on BCL2 gene translation was investigated by in vitro studies using primary KCOT culture cells. Results Using qRT-PCR, we observed miR-15a and/or miR-16-1 downregulation in the majority of the KCOT samples (24 of 28).We also observed higher BCL2 mRNA expression in 19 of 20 KCOT frozen samples and moderate to high Bcl-2 immunopositivity in the basal layer cells of 16 of 18 paraffin embedded KCOTs (median: 42.6 %). In vitro over-expression of miR-15a/16-1 in human KCOT-1 primary cell cultures resulted in a decrease in Bcl-2 protein expression. Furthermore, all five paired KCOTs collected before and after marsupialization treatment exhibited an increase in miR-15a after the procedure. Conclusions Our results suggest that KCOT neoplastic cells exhibit an anti-apoptotic profile that may be related to lower miR-15a/16-1 expression. Additionally, we demonstrated that miRNA expression increases after marsupialization, implicating an etiological and therapeutic role of miRNAs in KCOT. © International Society for Cellular Oncology 2012.