Only occasional cases of Trichomonas spp. infection have been reported in neonates, and these usually represent vaginal infections with Trichomonas vaginalis acquired during passage down the birth canal. We report the case of a 2-week-old girl who was brought by her mother to the Children's Emergency Clinic at our institution for symptoms of lethargy and poor appetite. The neonate was subsequently diagnosed with herpetic encephalitis and developed increasing respiratory difficulty, requiring intubation. Routine viral culture of a nasopharyngeal wash showed no viral organisms, but trichomonads were abundant microscopically on the viral culture medium. Molecular studies identified the organism as T. vaginalis. The significance of this organism as a neonatal respiratory pathogen and its contribution to neonatal respiratory distress are discussed.