Purpose Hospitalized, medically complex patients with new tracheostomy are at risk for aspiration. This study reports incidence of aspiration in these patients with new tracheostomy and investigates possible risk factors for aspiration and silent aspiration in this patient population. Method Retrospective review of instrumental swallowing evaluations from hospitalized inpatients with new tracheostomy tubes to determine frequency of aspiration and silent aspiration and patient factors associated with aspiration. Patient variables including sex, age, reason for hospital admission, reason for tracheostomy, duration of intubation, time since tracheostomy placement, and tracheostomy cuff and cap status were examined as possible risk factors for aspiration and silent aspiration. Results Of the 272 patients with new tracheostomies who underwent instrumental swallowing evaluation, 59% aspirated on at least one consistency. Odds of aspiration were twice as high in patients with uncapped tracheostomy compared to closed (i.e., cap or speaking valve in place). Odds of aspiration were 3.4 times greater with patients who underwent tracheostomy for an oropharyngeal etiology (oropharyngeal or laryngeal tumor, surgery, or infection). Of the patients who aspirated, 81% aspirated silently on at least one consistency. Odds of silent aspiration was 4.5 greater with an uncapped tracheostomy. Conclusions Medically complex patients with new tracheostomy are at risk for aspiration and benefit from instrumental swallowing evaluations. Future prospective research is warranted to determine contributing factors responsible for this risk. Lastly, speech pathologists play an important role in the patient's recovery.