Determination of the following: (1) colonization and infection rates in children requiring long-term ventilation initially via a transtracheal tube and subsequently via a tracheotomy; (2) the number of infection episodes per 1,000 ventilation days, during both types of artificial airways; and (3) routes of colonization/infection of the lower airways, ie, whether the pathogenesis was endogenous (via the oropharynx) or exogenous (via the transtracheal tube or tracheotomy). Observational, cohort, prospective study over 2 1/2 years. Pediatric ICU (PICU), Royal Liverpool Children's National Health Service Trust of Alder Hey, a tertiary referral center. Twenty-two children requiring long-term mechanical ventilation initially transtracheally and subsequently via a tracheotomy. Nil. The lower airways were colonized in 71% of children during transtracheal ventilation; posttracheotomy, this was 95% (p=0.03). Children developed significantly fewer infections following colonization with a microorganism posttracheotomy (8/15 pretracheotomy vs 6/21 posttracheotomy; p=0.013). Throughout the study, there were a total of 17 episodes of infection, all of which were preceded by colonization. Haemophilus influenzae, Staphylococcus aureus, Acinetobacter baumannii, and Pseudomonas aeruginosa were the same four causative pathogens during mechanical ventilation both transtracheally and via tracheotomy. Forty-nine episodes of colonization were observed, 15 pretracheotomy and 34 posttracheotomy; of these, 12 (80%) and 19 episodes (56%), respectively, were primary endogenous, ie, present in the oropharynx on hospital admission and subsequently at tracheotomy. Only one colonization episode (7%) of exogenous pathogenesis was observed during transtracheal intubation, while 12 (35%) (p=0.02) occurred after tracheotomy. An equal number of secondary endogenous colonization episodes (two and three, ie, acquired in the oropharynx after PICU admission and after tracheotomy, respectively, were recorded. (1) Despite a high level of hygiene, exogenous colonization without subsequent infection was common. (2) Although all patients were colonized, the infection rate was lower after tracheotomy. This may be due to enhanced immunity (medically stable) and improved tracheobronchial toilet. (3) Microorganisms in children with tracheotomy differ from those in adults.