Pediatric oncology and hematology patients are at increased risk of developing healthcare associated infections (HAIs). We conducted a prospective surveillance study on children with cancer admitted to the pediatric hematology and oncology units at a public pediatric hospital in Mexico from January 2004 to December 2009. The incidence of HAIs and groups at greatest risk for HAIs were analyzed. The annual HAI incidence rate and incidence density were calculated. Risk factors such as site of infection, HAI types, and cancer diagnosis were studied. A total of 9420 patients participated, and 409 had HAIs (479 episodes). Annual HAI rates were 3.7 to 5.5 per 100 admissions and the incidence density was 5.75 to 6 HAIs per 1000 inpatient days annually. There were 272 (56.8%) bloodstream infections, 45 (9.4%) pneumonia cases, and 44 (9.2%) skin and soft tissue infections. Children with acute lymphoblastic leukemia had 37.2% and those with acute myeloid leukemia had 16.4% of the HAIs. A total of 11.5% of the HAIs were in children with osteosarcoma. The most common pathogens were Gram-negative bacteria. The HAI-associated mortality rate was 3.7%. Although the overall HAI rate is in line with published reports, the mortality rate was higher, suggesting the incorporation of more aggressive methods to treat infections at our hospital.