Introduction: Febrile neutropenia (FN) is a common complication of patients undergoing chemotherapy (QMT). Clinical presentation is varied, from mild fever to severe sepsis with invasive bacterial infection (IBI) or invasive fungal infection (IFI), with great impact on prognosis and patient mortality. Patients and Methods: Prospective cohort study of FN episodes in adult patients with acute leukemia (AL) or lymphoma (L), diagnosed and treated at the Hospital Clinico Universidad Catolica and Hospital Dr. Sotero del Rio in Santiago from April 2010 to January 2012. Results: 130 patients were included with 105 episodes of NF, with an incidence of 0.65 per 100 days of observation, higher in AL than L (1.31 vs 0.25, p = 0.001). Etiology or clinical focus was documented in 67 (63.8%) episodes, with IBI in 33 (31.4%) and IFI in 21(20%) cases. Mortality related to infection occurred in 4 (6.2%) patients. Conclusions: This study reports that the FN incidence and frequency of IBI and IFI during episodes are higher in AL vs. L. It is necessary to evaluate the impact of interventions to reduce its incidence, including the benefit and risk of using antibacterial and antifungal prophylaxis in high-risk subgroups.