We treated a patient with 6p partial deletion syndrome diagnosed after proteinuria was detected during developmental examination 3 years after birth. External anomalies included ocular hypertelorism, saddle nose, elongated philtrum, tent-like lips, and low-set auricles. Mental retardation was evident. The karyotype was 46,XX,del(6) (p.22.1-p22.3) with an interstitial deletion. The kidneys showed no abnormality on imaging such as hydronephrosis, atrophy, or malformation. Examination of a renal biopsy specimen disclosed focal segmental glomerulosclerosis. No cardiac anomaly or Rieger anomaly, which often are present in this syndrome, were noted.