A 3-week-old male infant, born full term without complication, developed septic arthritis of his left shoulder. His joint fluid, blood, and bone marrow were all positive for Escherichia coli. Urinalysis demonstrated pyuria. Urine culture obtained after one dose of ceftriaxone and several doses of nafcillin was negative. Work-up revealed a refluxing, right single ectopic ureter with severe hydroureteronephrosis and a non-functioning ipsilateral kidney. After appropriate management of the musculoskeletal infection, he underwent a right nephroureterectomy. Coliform septic arthritis is exceedingly rare in children, with only a few cases reported. We report the first case of septic arthritis with anomalous genitourinary tract development as the source of bacterial seeding. This report re-emphasizes the need to screen the urinary tract in all cases of pediatric gram-negative sepsis.