Background: Hypothermia is very prevalent in neonatal transport and can increase morbidity and mortality in this age group. Materials and Methods: In this study, all neonates transported from different parts of Bushehr province to Ali Asghar hospital during the second half (2007) were checked for axillary temperature on admission. Results: 328 neonates were entered to the study. The incidence of hypothermia was 47.6 percent. There was a significant relationship between hypothermia and transfer method (with or without incubator), gestational age, chronological age on admission, birth weight, Apgar score (P<0.0001) and neonatal outcome (P=0.001). Conclusion: Hypothermia leads to increased mortality in neonates and is related to prematurity and low birth weight and low Apgar score. Kangaroo mother care (KMC) is recommended instead of incubator care to prevent hypothermia during transfer.