Patients with brain injury are prone to bacterial colonisations because of mechanical ventilation during intensive care and the long-term retention of tracheostomical tubes during rehabilitation. Reduced levels of isolation, typical of rehabilitation, could also contribute to propagate colonisations. We evaluated the presence of bacteria through different stages of healthcare, their antibiotic resistances and their clinical impact in a rehabilitation setting. This retrospective study included all tracheostomised patients referred to the paediatric brain injury unit of the Scientific Institute IRCCS E. Medea (Italy) over a six-year period. Data were collected from antibiograms regarding the presence of bacterial species and antibiotic resistances; clinical data were collected from medical records. Antibiograms revealed bacteria and antibiotic resistances typical of intensive care, while prevalence patterns were characteristic for each species (P. aeruginosa and S. aureus prevailing in the acute setting, K. pneumoniae, A. baumannii and others in rehabilitation). Despite very frequent antibiotic resistances, consistent with Italian averages, we observed a limited clinical impact for these colonisations. We analysed risk factors correlating to the development of respiratory symptoms and found a role for the acute clinical course after brain injury (having undergone neurosurgery; duration of intensive care stay) as well as for rehabilitation (duration of coma). Our data suggest that, in a long-term perspective, an appropriate balance is yet to be found between patient isolation and social interactions, to control respiratory colonisations and antibiotic resistances without compromising rehabilitation. They also suggest that regular containment measures should be complemented by thorough training to non-medic personnel and parents alike.