The RQ values obtained for the BMP7, SMAD4, and CDH1 genes and miR-542-3p in ectopic tissue were analyzed in relation to the following clinical features of patients with endometriosis: age at time of diagnosis, stage of endometriosis (according to rASRM classifications), pelvic pain symptoms (according to the numerical rating scale—NRS), and concentrations of the biochemical parameters of CA-125 and HE4. This evidence concerns the gene WFDC2 and endometriosis.