Hypospadias is a rare congenital malformation of the urethra reported in cattle. The urethral lumen of male indigenous Korean calf is open along the ventral aspect of the penis in the perineal region. Renal abscess and renal stone formation causing urinary tact infection has not been reported in hypospadia calves. The objective of this study was investigation for renal abscess and renal stone formation through autopsy. Histopathological examination and laboratory tests were performed. At autopsy, the pustules were formed on the right renal cortex, and the renal medulla abscess were formed on right and left part of the renal pelvis. Histopathological finding, this case was diagnosed as severe acute suppurative and necrotizing pyelonephritis, and severe chronic interstitial nephritis with fibrosis and moderate multifocal acute cystitis with edema. Milky exudate of the kidney has been identified as Actinomyces meyeri using the VITEK-2 system for identification of bacteria, and the stone has been identified as carbonate apatite using FT-IR system for quantification analysis. This case report describe the hypospadias complicated with urinary tract infection due to carbonate apatite stones and Actinomyces meyeri.