Background Respiratory infections are one of the leading causes of morbidity and mortality worldwide: influenza is one of the predominant pathogens responsible. During 2010, Paraguay actively sought for pH1N1 case-patients to estimate the incidence of severe acute respiratory infections (SARI) and deaths associated with influenza.

Objective To determine the contribution of Influenza in patients hospitalised with clinical evidence of severe acute respiratory infections (SARI).

Methods During 1 January 2010–31 December 2010, hospital staff identified all case-patients who met the SARI definition of sudden onset fever, and cough or sore throat, with shortness of breath requiring hospitalisation. Physicians obtained nasal and pharyngeal swabs from case-patients and sent the samples to the Paraguay National Influenza Center for influenza testing by immunofluorescence and reverse transcriptase polymerase chain reaction.

Results Hospital staff identified 2145 SARI cases of which they tested 1581 (74%) for influenza. Of these 284 cases (18%) were positive for influenza. The most frequently subtypes identified viruses were Influenza A H3N2 71% (202/284), influenza A H1N1 14% (41/284), influenza B 14% (41/ 284). We estimated that the rate of influenza-associated mortality was 2.8/100 000 persons-year (py).

Conclusion Out findings suggest that influenza caused a significant burden and may warrant further investments in its control and prevention.