Background: Hypothermia is an important determinant of survival in newborns, especially among low-birth-weight ones. Prolonged hypothermia leads to edema, generalized hemorrhage, jaundice and ultimately death. This study was undertaken to examine the factors affecting transition from hypothermic state in neonates.Methods: The study consisted of 439 neonates hospitalized in NICU of Valiasr in Tehran, Iran in 2005. The neonates' rectal temperature was measured immediately after birth and every 30 minutes afterwards, until neonates passed hypothermia stages. In order to estimate the rate of transition from neonatal hypothermic state, we used multi-state Markov models with two covariates, birth weight and environmental temperature. We also used R package to fit the model.Results: Estimated transition rates from severe hypothermia and mild hypothermia were 0.1192 and 0.0549 per minute, respectively. Weight had a significant effect on transition from hypothermia to normal condition (95% CI: 0.1364-0.4165, P<0.001). Environmental temperature significantly affected the transition from hypothermia to normal stage (95% CI: 0.0439-0.4963, P<0.001).Conclusion: The results of this study showed that neonates with normal weight and neonates in an environmental temperature greater than 28 °C had a higher transition rate from hypothermia stages. Since birth weight at the time of delivery is not under the control of medical staff, keeping the environmental temperature in an optimum level could help neonates to pass through the hypothermia stages faster.