We conducted a retrospective study to analyze various aspects of tracheotomy in children with abnormal laryngotracheal anatomy, a congenital cardiac anomaly, both, or neither. Our study population consisted of 53 children who had undergone tracheotomy performed by a single otolaryngologist; 12 patients had abnormal laryngotracheal anatomy and 9 had a cardiac anomaly. Mean operative times were significantly longer in both of these groups than they were in children with normal anatomy (69 vs. 50 min; p < 0.0001) and in children with no cardiac anomaly (65 vs. 53 min; p < 0.05). Post-tracheotomy survival at 1 and 2 years for children with a cardiac anomaly was significantly worse than survival for those without (44 vs. 91%; p < 0.001). Likewise, children who had been intubated for 10 days or more had significantly worse survival than did those who were intubated for less than 10 days (55 vs. 95%; p < 0.001). Finally, we found that the patients with prolonged intubation, respiratory failure, and a cardiac surgical history had higher mortality rates associated with tracheotomy.