Background Children with tracheostomies are at an increased risk of bacterial respiratory tract infections. Infections caused by multidrug-resistant organisms (MDROs) are more difficult to treat and can result in severe complications. We investigated the risk factors and sequelae of MDRO positivity in tracheostomy and chronic ventilator-dependent children. Methods We performed a retrospective chart review of 75 tracheostomy and chronic ventilator-dependent children at St. Louis Children’s Hospital. Data on demographics, respiratory cultures, hospitalizations, emergency department (ED) visits, and antibiotic usage were collected. We determined the frequency of MDRO positivity and compared the number of hospitalizations, number of ED visits, and antibiotic usage in patients with and without MDRO-positive cultures. Patient clinical variables were analyzed before and after MDRO acquisition. Results We found 75.7% (56/74) of our participants had an MDRO-positive culture, with methicillin-resistant Staphylococcus aureus (MRSA, n=36, 64%) and Pseudomonas aeruginosa (n=8, 14%) being the most commonly detected organisms. Patients with MDRO-positive cultures had a greater number of annual non-pulmonary admissions [OR=1.99, 95% CI (1.21-3.29), P= 0.008], inpatient antibiotic courses [OR=1.27, 95% CI (1.07-1.50), P=0.006], total antibiotic courses [OR=1.26, 95% CI (1.08-1.48), P= 0.004], and chronic antibiotic use [OR=2.31, 95% CI (1.12-4.74), P=0.03] compared to MDRO-negative participants. Patients that acquired MDROs during the study period subsequently required increased outpatient antibiotics [P= 0.006] but did not have increased pulmonary admissions or ED visits. Conclusion Frequent antibiotic usage and hospitalizations increase the risk of MDRO acquisition in children with tracheostomies and ventilator-dependence. Further antibiotic stewardship may help prevent resistant infections in technology-dependent children.