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Aim To describe characteristics and outcome of mechanically ventilated patients admitted to three newly established intensive care units (ICU) in Bosnia-Herzegovina and Serbia for 2009 H1N1 influenza infection. Methods The retrospective observational study included all mechanically ventilated adult patients of three university- affiliated hospitals between November 1, 2009 and March 1 2010 who had 2009 H1N1 influenza infection confirmed by real-time reverse transcriptase-polymerasechain- reaction (RT-PCR) from nasopharyngeal swab specimens and respiratory secretions. Results The study included 50 patients, 31 male (62%), aged 43 ± 13 years. Median time from hospital to ICU admission was 1 day (range 1-2). Sixteen patients (30%) presented with one or more chronic medical condition: 8 (16%) with chronic lung disease, 5 (10%) with chronic heart failure, and 3 (6%) with diabetes mellitus. Thirty-two (64%) were obese. Forty-eight patients (96%) experienced acute respiratory distress syndrome (ARDS), 28 (56%) septic shock, and 27 (54%) multiorgan failure. Forty-five patients (90%) were intubated and mechanically ventilated, 5 received non-invasive mechanical ventilation, 7 (14%) high-frequency oscillatory ventilation, and 7 (14%) renal replacement therapy. The median duration of mechanical ventilation was 7 (4-14) days. Hospital mortality was 52%. Conclusion Influenza 2009 H1N1 infection in three southeast European ICUs affected predominantly healthy young patients and was associated with rapid deterioration after hospital admission and severe respiratory and multiorgan failure. These emerging ICUs provided contemporary ICU services, resulting in case-fatality rate comparable to reports from well-established ICU settings.