Preterm infants have enhanced, but ill-defined susceptibility to severe respiratory syncytial virus (RSV) infection. In these experiments, we used quantitative polymerase chain reaction (qPCR) to compare laser captured microdissection (LCM) retrieved pulmonary epithelia to whole lung homogenates to evaluate the developmental expression of innate immune genes (surfactant protein A [SP-A] and sheep beta-defensin-1 [SBD1]). In whole lung homogenates of developing lambs (80%, 90% and term gestational age), SP-A mRNA expression generally increased with age (p<0.05). Detection of SBD1 mRNA expression was rare in gestation with more detectable expression at term birth. Using LCM and immunofluorescence, CD208+ cells (type II cells) and bronchiolar epithelium had increased SP-A mRNA expression with age (p<0.05) while bronchial epithelium had detectable but nonsignificant alterations in expression. SBD1 expression was sporadic in gestation at all anatomic levels but did show developmental increase in bronchiolar epithelium (p<0.05). Interestingly, bronchial expression was absent in older lambs. Innate immune genes can show cellular and age-dependent differences in mRNA expression and LCM can increase the sensitivity and cellular localization of expression. Supported in part by the NIH NAIAD Awards 5R01 AI062787-02 and 5K08 AI055499-03, USDA/CREES/NRI-CGP 2003-35204-13492, and the JG Salsbury Endowment.