Introduction Children with tracheostomy have an increased risk of bacterial colonization and infections of the lower respiratory tracts. This study aimed to investigate the effects of nebulized antibiotics on the bacterial load, the need for oral antibiotic courses, the number of hospitalizations, and the length of stay in the intensive care unit in children with tracheostomy. Methods Children with tracheostomy and persistent bacterial colonization who were started on nebulized antibiotic therapy after a lower respiratory tract infection were included to the study. Nebulized gentamicin or colistin were used according to the results of tracheal aspirate cultures. Demographic and clinic characteristics were recorded from one year before until 12 months after initiating nebulized antibiotic treatment. Results Nebulized antibiotic treatment was initiated in 22 patients. Inhaled gentamicin was administered to 14 patients (63.6%) and colistin to 8 patients (36.4%). The median duration of treatment was 3 months (2-5 months). Following nebulized antibiotic treatment, median number of hospitalizations decreased from 2 (1-3.5) to 1 (0-1.5) (p=0.04). The median length of stay in the intensive care unit reduced significantly from 89.5 days (43-82.5) to 25 days (7.75-62.75) after starting nebulized antibiotics (p = 0.028). Following nebulized antibiotic treatment colony count also decreased (105 CFU/ml (105-106) vs. 6x104 CFU/ml (104-105); p=0.003). Conclusions Nebulize antibiotics are a reasonable treatment option for lower respiratory tract infections for tracheotomized children with persistent colonization. Further studies are needed to determine the main indications and the optimal duration and doses of the long-term nebulized antibiotic treatment in these patients.