BACKGROUND: The clinical significance and appropriate diagnostic evaluation of atypical glandular cells of undetermined significance (AGCUS) on cervicovaginal Papanicolaou test have not been well established. CASE: A 53-year-old woman with AGCUS underwent colposcopy, cervical biopsy, hysteroscopy, dilation and fractional curettage, and subsequently hysterectomy with bilateral salpingo-oophorectomy without abnormal findings. A repeat vaginal Papanicolaou test revealed malignant cells. Extramammary Paget's disease and urothelial carcinoma in situ were subsequently determined to be the source of the abnormal cells interpreted as AGCUS. CONCLUSION: AGCUS may be associated with extramammary Paget's disease and urothelial carcinoma. One should maintain a high index of suspicion for extragenital causes of persistent AGCUS.