Use of the PLEX-ID system can lead to a rapid molecular diagnosis in microbiology. To illustrate the clinical implications of this new diagnostic tool, we present the case of a 46-year-old patient admitted with severe respiratory failure and septic shock. Cryptococcal pneumonia was diagnosed by Fungi-Fluor™ staining of the bronchoalveolar lavage (BAL) and the patient tested positive for HIV. Unfortunately, he died 12h after admission despite intensive care support and treatment with broad-spectrum antibiotics, amphotericin B, and flucytosine. Retrospective use of the PLEX-ID on the BAL, bronchial aspirate, and blood yielded Cryptococcus neoformans in all fluids tested. Rapid molecular diagnosis with PLEX-ID, especially when performed on the blood of septic patients, may reduce the time to adequate treatment and limit the number of diagnostic procedures needed.