Abstract Background Lower respiratory tract infections (LRTI) are a very serious complication in children with cancer, with high morbidity and mortality, due to viral infections, followed by bacterial and fungal organisms. These patients with cancer are undergoing chemotherapy that damages their mucosal barrier and respiratory epithelium, and course with profound or severe neutropenia. Thus, they are high-risk to develop severe respiratory infections acquired from the community. However, the clinical characteristics, etiological agents, finding on computed tomography (CT) and outcomes of the LRTI in immunocompromised patients are not well known, these are necessary in order to start adequate management including empirical antimicrobial therapy and supplementary oxygen therapy. Methods Children with cancer who were attended in the pediatric emergency room due to fever (>38°C) and presence of respiratory symptoms such as increased breath rate, cough, O2Sat <93%, and needed to supplementary oxygen were included. To analyze the cases of children with cancer and LRTI we documented the data regarding to clinical presentation, detection of respiratory virus and findings in the CT. Data such age, sex, oncological diagnosis, absolute neutrophil count. The detection of nucleic acid of respiratory virus was performed by qPCR, whereas the identification galactomannan in serum was done for fungal diagnosis, and clinical presentation was initial used for diagnosis of bacterial LRTI. The findings on TC were included to integrate all the LRTI etiological diagnosis. The outcomes recorded were to need supplementary oxygen therapy (nasal cannula, high-flow nasal cannula or mechanical ventilation), ICU admission, and mortality on the follow for all patient included in the study. A descriptive statistical analysis was performed to estimate frequency of the etiological agents, outcomes, and mortality rate. Results A total of 10 children with cancer and severe LRTI were followed up, 60% female sex, age 5.5 years (range, 1-16 <); 80% had acute leukemias and 20% lymphoma. Seven (70%) children were diagnosed with bacterial LRTI, whereas two (20%) and one (10%) were viral LRTI-diagnosed. The finding in the CT were the follow: bilateral patchy consolidation and ill-defined small nodules for viral infection, centrilobular nodules and bronchial wall thickening for bacterial infection and scattered nodules or patchy focus for fungal infection. In respect to clinical presentation 90% had fever, 100% had cough, and 100% had O2Sat <93%. Of these patients 60% were presented with profound and 20% with severe neutropenia (p<0.05); 30% had required high-flow oxygen and 10% mechanical ventilation; and three (30%) patients required care in ICU. The mortality rate for severe LRTI was 30%. Conclusion Children with cancer and profound or severe neutropenia are in high-risk to develop severe LRTI and they have high mortality. The finding on the CT can help to start on adequate management for LRTI in immunosuppressed pediatric patients.