Aim To analyze the 2009/2010 epidemiological data of patients hospitalized for confirmed pandemic influenza in Slovenia. Methods We conducted a retrospective analysis of health statistical data collected in an electronic data set Diagnosis-related Group system. Data on age, sex, primary and secondary diagnoses, duration of hospital stay, admission to the intensive care unit, disease outcome, and the week of the admission to the hospital were extracted for patients diagnosed with confirmed influenza virus infection. Results A total of 748 (hospitalization rate 37.4/100,000) patients diagnosed with confirmed influenza virus infection were admitted to 19 public hospitals and 7 private acute care providers during the period from September 28, 2009 to April 11, 2010. The highest admission rate was recorded for mid-November 2009. Out of 748 hospitalized patients, 411 (55%) were children younger than 15 years. Influenza was coded as the primary diagnosis in 536 patients. In 35% of the patients, influenza caused viral pneumonia. Fewer than one third of patients (28%) had a pre-existing chronic disease and/or condition predisposing them to complicated or adverse outcomes of influenza, most frequently chronic lung diseases, mainly asthma. A median hospital stay was 2 days for children and 5 days for adult patients. Longer hospitalization was required in patients who had a secondary diagnosis of influenza. Older male individuals suffering from pneumonia and chronic diseases were overrepresented among cases admitted to the intensive care units. Conclusions The epidemiological data extracted from the Diagnosis-related Group system in Slovenia were comparable with the data on pandemic patients published elsewhere.