BACKGROUND Neonatal transport is the most important component of regionalized perinatal health care system, but still there are no legal regulations on regionalized perinatal care and transport of sick new-borns in our country. Although hospital-based deliveries have increased, level I & II centers still have extremely limited resources. The need for the systematic transport from these far situated, level I & II centers with inadequate staffing and equipment, indicates the need for better regionalization with special care newborn units at district level. The present study was done to assess the effect of available Neonatal Transport System on morbidity and mortality of out born neonates; including modes, organized transport, special needs and care during transport. MATERIALS AND METHODS In this prospective observational study, we included all neonates (from birth to 28 days of life) born outside SAIMS hospital and referred to SAIMS, Neonatal Intensive Care Unit (NICU) for tertiary care centre for a period of one year. Cases who were found to be dead at the time of arrival to the institute were excluded from the study. RESULTS We observed that immediate and long-term outcome varies with the place of delivery, mode of transport, travelling distance and initial stabilization of the baby. We also found that biochemical and temperature disturbances are more common in babies transported on their own and a specialized neonatal transport service could improve the survival of these new-borns. CONCLUSION All Neonatal health care facilities should have some basic referral guidelines so that events like hypothermia, hypoglycaemia and hypoxia can be prevented.