Proteomic technology using SOMAmer (Slow Off-rate Modified Aptamer) nucleic acid-based protein-binding reagents allows for biomarker discovery.<b>Objectives:</b> We hypothesized that proteins and protein pathways in BAL fluid (BALF) would distinguish children with neuroendocrine cell hyperplasia of infancy (NEHI), surfactant dysfunction mutations, and other chILD diagnoses and control subjects.<b>Methods:</b> BALF was collected for clinical indications and banked in patients with chILD and disease control subjects using standardized protocols over 10 years.