Twelve healthy approximately 3-yr-old captive-born 4.5–9 kg American alligators (Alligator mississipiensis) each had bronchoscopy and tracheal washes performed four times during a 10-mo period to evaluate seasonal respiratory microbiology and cytology. Cytologic evaluation of most samples showed a small amount of mucus and low numbers of ciliated columnar epithelium, cubodial epithelium, and keratinized squamous cells. No bacteria or parasites were observed, and there was no seasonal variation in the cytology. No significant bacterial or fungal growth was identified in any season. Hematology performed in the spring and fall evaluations showed seasonal variation in the red blood cell count, hemoglobin concentration, mean corpuscular volume, mean corpuscular hemoglobin concentration, eosinophil count, and thrombocyte count. The lower respiratory tract (at the tracheal level) of healthy subadult alligators appears to be sterile, and cytology is similar to that described in domestic mammals.