Recurrent lower respiratory tract infections are among the most prevalent symptoms in secondary tracheomalacia due to mediastinal vascular anomalies (MVAs). It is not known whether this condition could result in persistent lower respiratory tract inflammation and subclinical infection. A retrospective study was performed on records of children with tracheomalacia due to MVAs and recurrent respiratory infections who underwent computed tomography scan, bronchoscopy, and bronchoalveolar lavage (BAL) as part of their clinical evaluation. Thirty-one children were included in the study: 21 with aberrant innominate artery, four with right aortic arch, one with double aortic arch, and five with aberrant innominate artery associated with right aortic arch. Cytological evaluation of bronchoalveolar lavage fluid showed increased neutrophil percentages and normal lymphocyte and eosinophil proportions. Microorganism growth was detected in 13 BAL samples, with a bacterial load ≥104 colony-forming units/mL in eight (25.8%) of them. Most isolates were positive for Haemophilus influenzae. Bronchiectasis was detected in four children, all with BAL culture positive for H. influenzae. Four patients underwent MVA surgical correction and 27 conservative management, i.e., respiratory physiotherapy in all and high-dose amoxicillin/clavulanic acid (40 mg/kg/day) for 2-4 weeks in those with significant bacterial growth. There was an excellent outcome in most of them. Neutrophilic alveolitis is detectable in secondary tracheomalacia but is associated with a clinically significant bacterial load only in a quarter of the patients. Caution should be used regarding inappropriate antibiotic prescriptions to avoid the emergence of resistance, whilst airway clearance maneuvers and infection preventive measures should be promoted.