Renalⁱ tract infections can occur, sometimes due to structural abnormalities and/or immune dysfunction. Common renal anomalies include renal dysplasiaⁱ, renal agenesisⁱ, horseshoe kidney, and ectopicⁱ kidney. Ureter abnormalities include obstruction, refluxⁱ, and duplication.

Undescended testes, hypospadiasⁱ, and small penis have all been reported. A significant amount of girls have premature breast development and, rarely, premature onset of puberty. Growth hormone deficiency, congenitalⁱ hypothyroidism, and insulin-dependent diabetes mellitus are all rare findings in KS.

Hypoglycemiaⁱ, hypoglycemia, is usually a short-lived problem in infants, but it has also been reported in older children. Vigilant monitoring during fasting periods for surgeries is essential.  Certain physical (structural) features associated with Kabuki syndrome could complicate the effects of anesthesia.  These may include: