BACKGROUND: Endotracheal intubation increases the risk for microaspiration of secretions around the tube cuff. Pepsin has been used as a biomarker for gastric aspiration. Amylase is a newer proposed biomarker for aspiration of oral contents. OBJECTIVE: To assess the presence of pepsin and amylase in paired oral-tracheal secretions of adult patients treated with mechanical ventilation. METHODS: In this descriptive study, paired samples of oral and tracheal secretions were obtained from adult patients at baseline and again within 4 hours when a need for endotracheal suctioning was assessed. Assays of pepsin and amylase were processed in a specialty diagnostic laboratory. RESULTS: The sample consisted of 10 men and 3 women with a median age of 56 years. The majority were intubated with a subglottic suction endotracheal tube (9 patients, 69%), receiving synchronized intermittent mandatory ventilation (10 patients; 77%), and receiving enteral feedings (11 patients; 85%) through a tube distally placed in the stomach (8 patients; 67%). Pepsin was present in oral secretions of 9 patients (69%), and in tracheal specimens of 7 patients (54%) at one or both sampling times. Amylase was detected in all patients' oral secretions and in tracheal secretions of 5 patients (38%) at one or both sampling times. CONCLUSIONS: Many patients had pepsin, amylase, or both in tracheal aspirates. Pepsin was more commonly detected than was amylase. Although the relationship of this finding to long-term outcomes was not assessed, findings indicate that microaspiration of oral and gastric secretions occurs frequently.