This study was designed to investigate the correlation between expression levels of cysteine aspartic protease-3 (caspase-3) and B-cell lymphoma gene-2 (Bcl-2) proteins in alveolar lavage fluid and the prognosis of infants with neonatal respiratory distress syndrome (RDS). A total of 150 infants with neonatal RDS undergoing alveolar lavages were divided into four groups: RDS1 (group A, n=42), RDS2 (group B, n=38), RDS3 (group C, n=38) and RDS4 (group D, n=32) according to their thoracic X-ray film grading. The oxygen uptake score, oxygenation saturation, mean airway pressure and expression levels of caspase-3 and Bcl-2 in alveolar lavage fluid of the infants in the four groups were measured and compared. Our results showed higher grading by thoracic X-rays in patients with increased oxygen uptake score, oxygenation index, mean airway pressure, caspase-3 expression level, hospital stay, complications and death rates in all groups; however, the expression levels of Bcl-2 were decreased in those cases, and the differences had statistical significance among the four groups (P<0.05). Analyses for correlation showed a caspase-3 positive area that was positively correlated with oxygen uptake score, oxygenation index and mean airway pressure (P<0.05); and a Bcl-2 expression level that was negatively correlated with oxygen uptake score, oxygenation index and mean airway pressure (P<0.05). Based on our findings, the severity of neonatal RDS is positively correlated with the concentration of caspase-3 in alveolar lavage fluid, and negatively correlated with the expression level of Bcl-2.