This study investigated the swallowing physiology of toddler-aged patients with long-term tracheostomies. Structural movements and motility of the pharyngeal stage of swallowing were studied in four toddlers ranging in age from 1:2 (years:months) to 2:9 with long-term tracheostomies. A patient aged 1:2 years with no tracheostomy served as a toddler model for comparison. Videofluoroscopic recordings of the patients' liquid and puree bolus swallows were analyzed for a) onset times for pharyngeal stage events, laryngeal vestibule closure, and tracheostomy tube movement; b) timeliness of swallow response initiation; and c) pharyngeal transport function. Results found differences in timing of pharyngeal stage movements between the tracheostomized patients and the patient with no tracheostomy. Laryngeal vestibule closure occurred before or within the same 0.033-s video frame as onset of upper esophageal sphincter (UES) opening in the patient with no tracheostomy, but occurred 0.033-.099 s after onset of UES opening in the tracheostomized patients. The time line required to close the laryngeal vestibule once the arytenoids began their anterior movement was longer in the tracheostomized patients than in the patient with no tracheostomy and was associated with laryngeal penetration. The patient with no tracheostomy displayed superior excursion of the arytenoid and epiglottis during the swallowing; the tracheostomized patients did not. No association was found between onset of tracheostomy tube movement and laryngeal vestibule closure. Delayed swallow response initiation was observed across tracheostomized patients at a mean frequency of 45% with associated penetration. Pharyngeal dysmotility was not observed. Findings supported the concept that long-term tracheostomy in toddler-aged patients affects swallowing physiology.