Background. Despite the growing share of neonatal mortality in under-5 mortality in the recent decades in India, most studies have focused on infant and child mortality putting neonatal mortality on the back seat. The development of focused and evidence-based health interventions to reduce neonatal mortality warrants an examination of factors affecting it. Therefore, this study attempt to examine individual, household, and community level factors affecting neonatal mortality in rural India. Data and methods. We analysed information on 171,529 singleton live births using the data from the most recent round of the District Level Household Survey conducted in 2007-08. Principal component analysis was used to create an asset index. Two-level logistic regression was performed to analyse the factors associated with neonatal deaths in rural India. Results. The odds of neonatal death were lower for neonates born to mothers with secondary level education (O R = 0.60, p = 0.01) compared to those born to illiterate mothers. A progressive reduction in the odds occurred as the level of fathers' education increased. The odds of neonatal death were lower for infants born to unemployed mothers (O R = 0.89, p = 0.00) compared to those who worked as agricultural worker/farmer/laborer. The odds decreased if neonates belonged to Scheduled Tribes (O R = 0.72, p = 0.00) or 'Others' caste group (O R = 0.87, p = 0.04) and to the households with access to improved sanitation (O R = 0.87, p = 0.02), pucca house (O R = 0.87, p = 0.03) and electricity (O R = 0.84, p = 0.00). The odds were higher for male infants (O R = 1.21, p = 0.00) and whose mother experienced delivery complications (O R = 1.20, p = 0.00). Infants whose mothers received two tetanus toxoid injections (O R = 0.65, p = 0.00) were less likely to die in the neonatal period. Children of higher birth order were less likely to die compared to first birth order. Conclusion. Ensuring the consumption of an adequate quantity of Tetanus Toxoid (TT) injections by pregnant mothers, targeting vulnerable groups like young, first time and Scheduled Caste mothers, and improving overall household environment by increasing access to improved toilets, electricity, and pucca houses could also contribute to further reductions in neonatal mortality in rural India. Any public health interventions aimed at reducing neonatal death in rural India should consider these factors.