Background: Acute rheumatic fever and rheumatic heart disease cause a high burden of disease in Fiji and surrounding Pacific Island countries, but little is known about the epidemiology of group A streptococcal (GAS) pharyngitis in the region. We designed a study to estimate the prevalence of carriage of beta-hemolytic streptococci (BHS) and the incidence of BHS culture-positive sore throat in school aged children in Fiji. Methods: We conducted twice-weekly prospective surveillance of school children aged 5 to 14 years in 4 schools in Fiji during a 9-month period in 2006, after an initial phase of pharyngeal swabbing to determine the prevalence of BHS carriage. Results: We enrolled 685 children. The prevalence of GAS carriage was 6.0%, while the prevalence of group C streptococcal (GCS) and group G streptococcal (GGS) carriage was 6.9% and 12%, respectively. There were 61 episodes of GAS culture-positive sore throat during the study period equating to an incidence of 14.7 cases per 100 child-years (95% CI, 11.2–18.8). The incidence of GCS/GGS culture-positive sore throat was 28.8 cases per 100 child-years (95% CI, 23.9–34.5). The clinical nature of GAS culture-positive sore throat was more severe than culture-negative sore throat, but overall was mild compared with that found in previous studies. Of the 101 GAS isolates that emm sequence typed there were 45 emm types with no dominant types. There were very few emm types commonly encountered in industrialized nations and only 9 of the 45 emm types found in this study are emm types included in the 26-valent GAS vaccine undergoing clinical trials. Conclusions: GAS culture-positive sore throat was more common than expected. Group C and group G streptococci were frequently isolated in throat cultures, although their contribution to pharyngeal infection is not clear. The molecular epidemiology of pharyngeal GAS in our study differed greatly from that in industrialized nations and this has implications for GAS vaccine clinical research in Fiji and other tropical developing countries.