We describe a case of a 55-year-old woman with polycystic kidney disease who received a living donor kidney transplant 16 years earlier and was on immunosuppressive therapy with satisfactory renal function. The donor was her mother. The patient presented with flank pain on the right side and macrohematuria, and noncontrast computed tomography and magnetic resonance imaging led to the diagnosis of tumors in the remaining right native polycystic kidney and ureter, as well as secondary retroperitoneal dissemination. We performed right radical nephrectomy and ureterectomy with extirpation of 2 metastases; the left native kidney remained intact. Histology showed squamous metaplastic changes and invasive epithelial neoplasm in the lumen of the renal pelvis and ureter with extensive squamous differentiation positive for nuclear p63 as squamous cell immunohistochemical marker. After surgery, an immunosuppressive therapy with methylprednisolone was administered, without calcineurin inhibitors and mycophenolate mofetil. Twelve months later the patient was still alive, with a glomerular filtration rate of 29 mL/min. Needs remain for further treatment modalities in patients with primary squamous cell carcinoma in nonfunctioning kidneys and improvements in imaging technique accuracy.