An eight-month-old boy who presented with a 15-day history of vomiting was revealed to be suffering from urinary tract infection and nephrocalcinosis caused by vitamin D intoxication. During the treatment of vitamin D intoxication (alendronate, 5 mg/day), he developed urinary tract infection and septic arthritis of the left hip joint. Escherchia coli was isolated from his blood, urine, and joint fluid culture. He was operated, joint drainage was performed and appropriate intravenous antibiotic treatment was given for four weeks. After discharge, a voiding cystoureterogram revealed grade 4 vesicoureteral reflux in the right ureter. Combination of complex urinary anomalies associated with stagnation of urine flow and altered urinary dynamics, and metabolic urinary anomalies, such as hypercalciuria/nephrocalcinosis, may facilitate the occurrence of rare systemic complications of urinary tract infection.