Using a multiple correction threshold of p<9.3×10−4 (0.05/54 CNVRs analyzed), we identified three loci strongly associated with endometriosis; a deletion in SGCZ on 8p22 (P = 7.3×10−4, OR = 8.5, Cl = 2.3–31.7), a deletion in MALRD1 on 10p12.31 (P = 5.6×10−4, OR = 14.1, Cl = 2.7–90.9), and a deletion at 11q14.1 (P = 5.7×10−4, OR = 33.8, Cl = 3.3–1651). The gene discussed is MALRD1; the disease is endometriosis.