Abstract Introduction An aberrant immunologic mechanism has been suggested to be involved in the pathogenesis of endometriosis. Nuclear factor-kB (NF-kB) plays a key role in the immune and inflammatory response and modulates cell proliferation, apoptosis, adhesion, invasion, and angiogenesis in many cell types involved in the development of endometriosis. We hypothesized a possible relationship between the NFKB1 promoter regulatory polymorphism and endometriosis and/or infertility. Methods A genetic association study comprising 172 infertile women with endometriosis, 77 women with idiopathic infertility and 189 controls was performed. Detection of the −94 insertion/deletion ATTG (rs28362491) polymorphism in the NFKB1 gene was done using the RFLP–PCR (Restriction Fragment Length Polymorphism–Polymerase Chain Reaction) technique. The results were statistically analyzed, and a p-value <0.05 was considered significant. Results Single-marker analysis revealed a significant association between the −94 insertion/deletion ATTG polymorphism and endometriosis-related infertility (p=0.014, OR=1.47, 95% CI=1.09–1.97), especially in moderate/severe disease cases. Considering the idiopathic infertility group, a significant association was also found (p=<0.001, OR=2.01, 95% CI=1.35–2.98), suggesting that the −94 insertion/deletion ATTG polymorphism is associated with endometriosis and/or infertility. Conclusion In the population sample studied, the −94 insertion/deletion ATTG polymorphism in the NFKB1 gene was positively associated both with moderate/severe endometriosis and idiopathic infertility.