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Background: Pertussis diagnosis may go unrecognized when other pathogens, such as respiratory syncytial virus (RSV) circulate. Methods: A prospective cross-sectional study was conducted in Lima, Peru from January 2009 to September 2010. A total of 596 children under 5 years old admitted with clinical diagnoses of acute respiratory infections were test for B. pertussis and RSV detection by polymerase chain reaction (PCR). Results: The pertussis toxin and IS481 genes were detected in 19.12% (114/596) of the cases and the respiratory syncytial viruses (RSV-A and RSV-B) were identified in 17.28% (103/596) of patients. Infants under 3 months old were the most frequently affected by this pathogens in 43% (49/114) and 35.9% (37/103) respectively. An increase of B. pertussis was observed from February to March and from October to November with a Seasonal index between 1.32-1.51 and 1.24-3.5 resp...