A full-term male neonate, weighing 2540 g at birth, was admitted to hospital on day 2 because of vomiting and severe dehydration. Duodeno-duodenostomy was performed on day 5 for congenital duodenal atresia. The child was well postoperatively until day 9, when he developed fever. Intermittent fever continued despite treatment with several antibiotics. He became seriously ill on day 15 and developed disseminated intravascular coagulation. Treatment with antifungal drugs (amphotericin B and 5-flucytosine) was effective for systemic candidiasis, but candida endophthalmitis developed. There was a persistent vitreous lesion in the left eye, which after cessation of therapy has been improving gradually. Systemic candidiasis and candida endophthalmitis should be considered in neonates who develop signs of sepsis postoperatively.