Newborn morbidity and mortality remains high despite a remarkable decline in the infant mortality and under five mortality rates in Nepal over the last decade (1996-2006). Research shows that newborns’ health outcome is associated with maternal and other factors. This study was designed to understand the factors that have an impact on three good newborn care practices: safe cord cutting, early breastfeeding and delayed bathing. The study used the interview data of 815 married women aged 15-49 years who delivered a live baby between February 2008 and February 2009, collected for the baseline survey of the Community-Based Maternal and Newborn Health program implemented in the Sindhuli district of Nepal. The mean age of the sample women was 26 years. Two-thirds of them were from disadvantaged indigenous caste/ethnicity groups, about 70% were uneducated and the majority were poor. Safe cord cutting, early breastfeeding and delayed bathing practices were studied for 803, 810 and 812 women respectively and 70.7%, 46.7%, and 16.6% of the eligible samples demonstrated the practices respectively. The logistic regression method was used to examine the association of independent factors with the outcome variables. Social gradient was found to be associated with all three practices. Rich women were more likely to demonstrate good practices and bearing a child at the prime age (20-34 years) was likely to result in safe cord cutting. Disadvantaged indigenous and ‘other’ caste/ethnicity women demonstrated unsafe cord cutting practices and dalit caste/ethnicity women demonstrated poor bathing practices. Maternal knowledge also emerged as a strong predictor of early breastfeeding and delayed bathing practices. Antenatal care from a SBA determined good breastfeeding and advice from a FCHV determined good bathing practices. The results showed that the uptake of antenatal and delivery services from a skilled birth attendant is unacceptably low in rural Nepal, which is a challenge for meeting the millennium development goals. The study recommends programmes for improving economic status as a key to improving newborn care practices. As the vast majority of the deliveries are still assisted by traditional birth attendants; including them in maternal health programmes is crucial. Increasing women’s access to a skilled birth attendant and boosting the spirit of the FCHVs to increase their efficiency is also recommended. Future research on newborn health should focus on identifying other determinants of newborn care practices and survival. Qualitative studies to understand the cultural perspectives of newborn care practices are also recommended.