The authors present a case of urinary infection by a non-tuberculous mycobacteria (NTM) species, Mycobacterium gordonae, in a renal transplant recipient. A 29-year-old female patient had persistent sterile pyuria after her second kidney transplant. An NTM, M. gordonae, was isolated, and the patient was started on antituberculous treatment, with resolution of leukocyturia. Ureteral stenosis with hydronephrosis and deterioration of allograft function was diagnosed later on and, despite the introduction of intraureteral catheter and resolution of hydronephrosis, there was no recovery of baseline renal function. She ultimately resumed dialysis after a severe pyelonephritis. The authors discuss the problems of establishing diagnosis of infection (versus colonization) by NTM and highlight the difficulty of treating these infections, especially because of the possible interaction with immunosuppressant agents, facilitating anti-allograft immune response.