Although gender-based health disparities are prevalent in India, very little data are available on care-seeking patterns for newborns. In total, 255 mothers were prospectively interviewed about their perceptions and action surrounding the health of their newborns in rural Uttar Pradesh, India. Perception of illness was significantly lower in incidence (adjusted odds ratio=0.56, 95% confidence interval 0.33-0.94) among households with female versus male newborns. While the overall use of healthcare providers was similar across gender, the average expenditure for healthcare during the neonatal period was nearly four-fold higher in households with males (Rs 243.3 +/- 537.2) compared to females (Rs 65.7 +/- 100.7) (p=0.07). Households with female newborns used cheaper public care providers whereas those with males preferred to use private unqualified providers perceived to deliver more satisfactory care. These results suggest that, during the neonatal period, care-seeking for girls is neglected compared to boys, laying a foundation for programmes and further research to address gender differences in neonatal health in India.