Equine endometrosis (endometrial fibrosis) is a degenerative chronic process that occurs in the uterus of the mare and disturbs proper endometrial function. Fibrosis is attributed to excessive deposition of extracellular matrix (ECM) components. The turnover of ECM is mediated by matrix metallopeptidases (MMP). Previously, it was shown that cytokines modulate MMP expression in other tissues and may regulate fibrosis indirectly by attracting inflammatory cells to the site of inflammation and directly on various tissues. However, the regulation of MMP expression in equine endometrosis is still relatively unknown. Thus, our aim was to determine if interleukin (IL)-1β and IL-6 regulate ECM, MMPs, or their inhibitors (TIMPs) and whether this regulation differs during endometrosis in the mare. Endometrial fibrosis was divided into four categories according to severity: I (no degenerative changes), IIA (mild degenerative changes), IIB (moderate degenerative changes) and III (severe degenerative changes) according to Kenney and Doig classification. Endometrial explants (n = 5 for category I, IIA, IIB and III according to Kenney and Doig) were incubated with IL-1β (10 ng/ml) or IL-6 (10 ng/ml) for 24 h. Secretion and mRNA transcription of collagen type 1 (Col1a1) and type 3 (Col3a1), fibronectin (Fn1), Mmp-1, -2, -3, -9, -13, Timp-1, -2 were analyzed by real-time PCR and ELISA, respectively. IL-1β treatment up-regulated secretion of COL1, MMP-2, TIMP1, and TIMP2 in category I endometrial fibrosis tissues (P < 0.05). IL-6 treatment up-regulated secretion of ECM, MMP-2, and MMP-3 and down-regulated secretion of MMP-9 in category I tissues (P < 0.05). In category IIA tissues, IL-1β and IL-6 treatment up-regulated secretion of COL3 (P < 0.05; P < 0.05), and IL-6 treatment also down-regulated secretion of MMP-9 (P < 0.05). In category IIB tissues, IL-1β treatment down-regulated secretion of COL3 (P < 0.05) and up-regulated secretion of MMP-3 (P < 0.01), while IL-6 treatment up-regulated secretion of MMP-3, MMP-9, and MMP-13 (P < 0.05). In category III tissues, IL-1β treatment up-regulated secretion of COL1, MMP-1, MMP-9 and TIMP-2 (P < 0.05), and IL-6 up-regulated secretion of all investigated ECM components, MMPs and TIMPs. These results reveal that the effect of IL-1β and IL-6 on equine endometrium differs depending on the severity of endometrial fibrosis. Our findings indicate an association between inflammation and development of endometrosis through the effect of IL-1β and IL-6 on expression of ECM components, MMPs, and TIMPs in the mare.