PC are a main cause of death following HSCT in children. We aimed to evaluate early predictors of mortality in paediatric recipients with PCs. A retrospective observational study of 35 patients with 49 episodes of PI on chest radiography (of 124 patients) who had undergone HSCT at a tertiary university hospital between January 2011 and December 2012 was performed. During follow-up (median 26.1 months), 15 episodes led to death (30.6%). An aetiologic diagnosis was made by non-invasive tests in 24 episodes (49.0%) and by adding bronchoalveolar lavage and/or lung biopsy in 7 episodes with diagnostic yield (77.8%, P = .001). Thus, a specific diagnosis was obtained in 63.3% of the episodes. Aetiology identification and treatment modification after diagnosis did not decrease mortality (P = .057, P = .481). However, the number of organ dysfunctions at the beginning of PI was higher in the mortality group, compared to the survivor group (1.7 ± 1.2 vs 0.32 ± 0.59; P = .001). Hepatic dysfunction (OR, 11.145; 95% CI, 1.23 to 101.29; P = .032) and neutropaenia (OR, 10.558; 95% CI, 1.07 to 104.65; P = .044) were independently associated with risk of mortality. Therefore, hepatic dysfunction and neutropaenia are independent early predictors of mortality in HSCT recipients with PCs.