Blood culture collection from outpatients < age 36 months with high fever (> 40º C, rectal) became a standard of ambulatory care in Emergency Rooms (ERs) of the 3 government Children’s Hospitals in Chile’s Metropolitan Region (MR) in 1999; thereafter, invasive pneumococcal disease (IPD) incidence doubled over preceding years’ estimates limited to hospitalizations. We studied IPD among children with moderate (>39ºC but 39º but 0.05). Extrapolating these rates to all ER outpatients < age 36 months with moderate and high fever, we estimate the true burden as 95 and 39 cases, respectively. The burden of pediatric IPD in the MR is currently underestimated because bacteremias among ER outpatients with moderate fever are not detected. If blood cultures were systematically collected from outpatients with moderate fever, recorded pediatric IPD burden would rise > 2-fold. However, economic and logistical constraints preclude such a practice.