Background Globally, respiratory infections are the primary cause of illness in developing countries, specifically among children; however, an etiological agent for many of these illnesses is rarely identified.Objectives Our study aimed to estimate the frequency of human bocavirus (HBoV) infection among pediatric populations in Argentina, Nicaragua and Peru.Methods We conducted a cross-sectional study using stored samples of an influenza-like illness surveillance program. Irrespective of previous diagnosis, nasopharyngeal or nasal swab specimens were randomly selected and tested using real-time PCR from three sites during 2007 from patients younger than 6 years old.Results A total of 568 specimens from Argentina (185), Nicaragua (192) and Peru (191) were tested. The prevalence of HBoV was 10.8% (95% CI: 6.3; 15.3) in Argentina, 33.3% in Nicaragua (95% CI: 26.6; 40.1) and 25.1% in Peru (95% CI: 18.9; 31.3).Conclusions These findings demonstrate circulation of HBoV in Argentina, Nicaragua and Peru among children with influenza-like symptoms enrolled in a sentinel surveillance program. © 2010 Blackwell Publishing Ltd.