To investigate the relationship between pregnancy intendedness and utilization of recommended prenatal care for mothers and vaccinations for children against six vaccine preventable diseases in rural India using a prospective dataset. To examine the association between pregnancy intention and neonatal and infant mortality in rural India. The study is based upon a prospective follow-up survey of a cohort selected from the National Family Health Survey 1998–1999, carried out in 2002–2003 in rural areas of four Indian states of Bihar, Jharkhand, Maharashtra and Tamil Nadu. Data for 2108 births for which pregnancy intendedness was assessed prospectively was analyzed using bivariate analysis, logistic regressions and discrete-time survival analysis. Mothers reporting unwanted births were 2.32 (95% CI: 1.54–3.48) times as likely as mothers reporting wanted births to receive inadequate prenatal care. Moreover, unwanted births were 1.38 (95% CI: 1.01–1.87) times as likely as wanted births to receive inadequate childhood vaccinations. Likewise, births that were identified as mistimed/unwanted had 83% higher risk of neonatal mortality compared to wanted births. The association between pregnancy intendedness and infant mortality was only marginally significant. This is the first study of its kind which has investigated the relationship between prospectively assessed pregnancy intendedness and early childhood mortality in rural India. The study provides additional and more conclusive evidence that unwanted births are disadvantaged in terms of maternal and child health outcomes. Findings argue for enhanced focus on family planning to reduce the high prevalence of unintended pregnancy in rural India.