BACKGROUND: The first positive patient with influenza A (H1N1) was recorded in March 2009 and the pandemic continued with new outbreaks throughout 2010. This study's objective was to quantify the total cost of inpatient care and identify factors associated with the increased cost of the 2009-2010 influenza A pandemic in comparison with nonviral respiratory infection.METHODS: In total, 133 positive and 103 negative H1N1 patients were included from three tertiary care hospitals during the two waves of H1N1 in 2009 and 2010. The health costs for protective equipment and pharmaceuticals and hospitalization (medications, laboratory, and diagnostic tests) were compared between H1N1 positive and negative patients.RESULTS: The objective of the study was to quantify the means of daily and total costs of inpatient care. Overall, cost was higher for H1N1 positive (€61,0117.72) than for H1N1-negative patients (€464,923.59). This was mainly due to the protection measures used and the prolonged hospitalization in intensive care units. In H1N1-negative patients, main contributors to cost included additional diagnostic tests due to concern regarding respiratory capacity and laboratory values, as well as additional radiologic and microbial culture tests. The mean duration of hospitalization was 841 days for H1N1 positive and 829 days for negative patients.CONCLUSION: Cost was higher in H1N1 patients, mainly due to the protection measures used and the increased duration of hospitalization in intensive care units. An automated system to monitor patients would be desirable to reduce cost in H1N1 influenza.