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 5years 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 3months 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 and 1.51 and 1.24-3.5 respectively. Conclusions: Epidemiologic surveillance for B. pertussis is essential in Peru, especially in children that could most benefit from the vaccine. B. pertussis should be suspected in infants hospitalized for acute respiratory symptoms for early treatment and prevent complications.