The World Health Organization (WHO) has questioned the sensibility of RT-PCR analysis for H1N1 in pharyngeal swab sample, encouraging analysis on samples from the lower respiratory tract. We routinely monitor H1N1 infection on three compartments: pharyngeal swab, subglottic aspiration, and bronchoalveolar lavage. In our experience, bronchoalveolar lavage at admission was positive in all patients while pharyngeal swab resulted positive in only 75% of cases.