OBJECTIVES: This study aimed to identify the most important factors affecting the total cost and the length of stay (LOS) of neonates who were hospitalized in six neonatal intensive care units (NICUs) in Greece. METHODS: The study sample consisted of 218 neonates who entered the NICUs of six maternity, pediatric and general hospitals, of Greece. Multivariate Regression analysis was performed in order to examine the factors affecting the LOS and the total cost of hospitalization. Data on mother and father educational and occupational status, type and number of delivery, place of residence (rural or urban), age of the mother, birth weight and the gestational age of the infants were available. The costs used for the analysis, emerged from a detailed cost analysis, bottom up approach, based on daily consumption of each neonate for the whole period of hospitalization, until discharge of the hospital. Bootstrap simulation was used with 1000 iterations in order to check for the stability of the cost analysis. RESULTS: Factors influencing the LOS (in days) and the total cost (in Euro) were identical in both regression models. Factors for LOS were the type of the hospital, since in the pediatrics hospitals neonates stayed longer than in the maternity hospitals (coefficient 17.44; 95%CI 4.61 to 30.28, p=0.004) and the birth weight of the neonate (coefficient 25.03; 95%CI: 8.304 to 41.77, p=0.004). Factors for the total cost were the length of stay (coefficient 228.11; 95%CI: 218.53 to 237.68, p<0.001), the type of the hospital (coefficient 993.72; 95%CI 301.03 to 1686.42, p=0.005) and birth weight of the infant (coefficient 1528.07; 95%CI 700.61 to 2355.54, p<0.001). CONCLUSIONS: The findings, as expected, proved that the lower the birth weight, the more prolonged and more costly the hospitalization. Differences in the type and organization between hospitals need further attention.