We identified <i>miR-301a-3p</i> as a possible marker of discrimination between two types of cystitis and its target gene, nuclear factor-κB (NF-κB) suppressing factor (<i>NKRF</i>).<h4>Conclusion</h4>Our results show that miRNA expression and its RA-validated targets, and enriched signaling pathways, differ between the two types of cystitis and might depend on the type of bladder inflammation. Here, NFKB1 is linked to chronic cystitis.