ABSTRACT: To quantify the incidence of and risk factors for neonatal jaundice among infants referred for care from a rural, low-resource, population-based cohort in southern Nepal.Study participants were 18,985 newborn infants born in Sarlahi District in southern Nepal from May 2003 through January 2006 who participated in a cluster-randomised, placebo-controlled, community-based trial to evaluate the effect of newborn chlorhexidine cleansing on neonatal mortality and morbidity. Jaundice was assessed based on visual assessment of the infant by a study worker and referral for care. Adjusted relative risks (RR) were estimated to identify risk factors for referral for neonatal jaundice using Poisson regression.The incidence of referral for neonatal jaundice was 29.3 per 1000 live births (95% confidence interval: 26.9, 31.7). Male sex, high birth weight, breastfeeding patterns, warm air temperature, primiparity, skilled birth attendance, place of delivery, prolonged labour, oil massage, paternal education and ethnicity were significant risk factors (P-values < 0.01). After multivariable adjustment, sex, birth weight, difficulty feeding, prolonged labour, primiparity, oil massage, ambient air temperature and ethnicity remained important factors. Among infants with difficulty feeding, exclusive breastfeeding was a risk factor for neonatal jaundice, whereas exclusive breastfeeding was protective among infants with no report of difficulty feeding.Several known risk factors for neonatal jaundice in a low-resource setting were confirmed in this study. Unique observed associations of jaundice with ambient air temperature and oil massage may be explained by the opportunity for phototherapy based on the cultural practices of this study population. Future research should investigate the role of an infant's difficulty in feeding as a potential modifier in the association between exclusive breastfeeding and jaundice.