Background Cases of bilirubin encephalopathy became sporadic since the introduction of phototherapy. Less aggressive treatment guidelines were introduced in the Netherlands in 1997. In the last decades there is an increasing number of cases of bilirubin encephalopathy in international literature. Aim To determine the incidence of severe hyperbilirubinaemia in newborns in the Netherlands and to identify associated risk factors. Methods Severe hyperbilirubinaemia was included in the Dutch paediatric surveillance (NSCK) from July 2005 until June 2007. Dutch paediatricians were asked to report term infants with hyperbilirubinaemia (>500 μmol/l). They received questionnaires requesting further information. Results There were 25 term infants reported (incidence: 6–7/100.000) The maximum bilirubin level was 784 μmol/l. 96% of cases presented from home. 44% were non-Caucasian, 73% were breast fed. Common causes were blood group incompatibility, feeding difficulties and haematomas related to birth-trauma. All infants were treated with phototherapy and 11 received an exchange transfusion. In 7 infants an MRI was performed, 3 showed pathognomic abnormalities. Furthermore, in most infants an AABR/BERA was performed, showing hearing deficits in 19%. So far, four children have a severely adverse neurological outcome and one child has a mild developmental delay. However, (long-term) neurological outcome of some infants is yet unknown. Conclusion This is the first large prospective population based study of the incidence and causes of severe hyperbilirubinaemia in term newborns in the Netherlands. Risk factors should be taken into account and community-based surveillance should be more appropriate, especially in high-risk cases. This preventable disorder has significant impact on neurological development.