Fungal organisms are one of the important factor in nosocomial urinary tract infections caused by endo-urological procedures. Herein we report a case of pyelonephritis caused by Paecilomyces variotti in a 14-month-old child following an uriner tract operation. He had operation in 3.5-month-old for reason of ureteropelvic junction obstruction. Approximately two months after the operation a tissue fragments ejected from urinary tract. The patient admitted to our hospital because of bimonthly recurrence was occured. This tissue fragment was sent for fungal studies to our department. Direct microscopy revealed hyphae. P. variotii was isolated from discarded tissue fragments. Cure was achieved by 2 mg / kg / day for 15 days treatment with amphotericin B.