BackgroundThe presence of endometriosis in the kidney is extremely rare. We report a case of endometriosis in renal parenchyma incidentally found in a malfunctioning kidney removed because of xanthogranulomatous pyelonephritis.Case presentationA 53-year-old Chinese premenopausal woman presented with intermittent right flank pain for many years. Imaging studies revealed a contracted non-functioning right kidney and a perinephric abscess. The contracted kidney was considered to have resulted from chronic pyelonephritis. The abscess was drained. The patient subsequently underwent a right nephrectomy. Histology revealed endometriosis of renal parenchyma in addition to xanthogranulomatous pyelonephritis and a perinephric abscess. No evidence of endometriosis was identified at the pelvic site. The patient was symptom-free after operation.ConclusionEndometriosis is a common benign condition in women of reproductive age that is characterized by the presence of endometrial glands and stroma outside the uterine cavity, which affects either genital or extragenital sites. Involvement of the urinary tract is rare. Among the urinary tract endometriosis, only a few cases involve the kidney. Renal endometriosis is difficult to diagnose; a final diagnosis relies on the pathohistologic findings. Treatment involves hormonal manipulation or a hysterectomy with bilateral salpingo-oophorectomy. Whether a nephrectomy required depends on the level of renal function. Although extremely rare, renal endometriosis should be part of the differential diagnostic spectrum when a contracted, non-functioning kidney is present. Early diagnosis might have prevented an unnecessary nephrectomy in cases of uncomplicated renal endometriosis.