Objective Better phenotyping of the heterogenous bronchiolitis syndrome may lead to targeted future interventions. This study aims to identify severe bronchiolitis profiles among hospitalised Australian Indigenous infants, a population at risk of bronchiectasis, using Latent Class Analysis (LCA). Methods We included prospectively collected clinical, viral and nasopharyngeal bacteria data from 164 Indigenous infants hospitalised with bronchiolitis from our previous studies. We undertook multiple correspondence analysis (MCA) followed by LCA. The best‐fitting model for LCA was based on adjusted Bayesian information criteria and entropy R2. Results We identified five clinical profiles. Profile‐A's (23.8% of cohort) phenotype was previous preterm (90.7%), low birth‐weight (89.2%) and weight‐for‐length z‐score <‐1 (82.7% from combining those with z‐score between ‐1 and ‐2 and those in the z‐score of <‐2 group) previous respiratory hospitalisation (39.6%) and bronchiectasis on chest high‐resolution computed tomography scan (35.4%). Profile‐B (25.3%) was characterised by oxygen requirement (100%) and marked accessory muscle use (45.5%). Infants in profile‐C (7.0%) had the most severe disease, with oxygen requirement and bronchiectasis in 100%, moderate accessory muscle use (85% vs 0‐51.4%) and bacteria detected (93.1% vs 56.7‐72.0%). Profile‐D (11.6%) was dominated by rhinovirus (49.4%), mild accessory muscle use (73.8%) and weight‐for‐length z‐score <‐2 (36.0%). Profile‐E (32.2%) included bronchiectasis (13.8%), RSV (44.0%), rhinovirus (26.3%) and any bacteria (72%). Conclusion Using LCA in Indigenous infants with severe bronchiolitis, we identified 5 clinical profiles with one distinct profile for bronchiectasis. LCA can characterise distinct phenotypes for severe bronchiolitis and infants at risk for future bronchiectasis, which may inform future targeted interventions.