OBJECTIVE To investigate the association between low Apgar score and the development of cholestasis. METHODS Seventy-seven cholestatic infants, all referred to our tertiary centre and born between 1987 and 1996 were studied. Twenty-eight patients had biliary atresia (BA), 36 had various intrahepatic disorders and for 13 patients the aetiology of the cholestasis was unknown. Data on gestational age, mode of delivery, Apgar score and birthweight for the cholestatic infants and 1,118,270 control subjects born during the same time period were obtained from the Swedish Medical Birth Registry. If the Apgar score of the cholestatic patient was <7 at 1 min and/or <9 at 5 min and/or <9 at 10 min of age the available medical records were reviewed for signs of neonatal distress. RESULTS Five cholestatic patients, all of them premature, fulfilled the Apgar criteria. For two of them the low Apgar score and need for immediate resuscitation were explained by major surgical problems. The other three patients, two with biliary atresia (BA) and one with Alagille syndrome, had clinical signs of neonatal distress. The incidence of low Apgar score in BA patients was 7% and in cholestatic patients without known aetiology 0%, neither figure differing significantly from that of the of the control group (2.6%). CONCLUSIONS Low Apgar score is not more common in any of the cholestatic groups than in the general Swedish population of newborns. We suggest that aetiological associations other than low Apgar score need to be considered in infants with cholestasis of unknown cause.