The diagnosis of invasive fungal infections remains challenging despite the advent of new tools. Among biomarkers, twice-weekly screening for serum galactomannan remains valuable despite the persistence of numerous false positives and false negatives in new, non-neutropenic populations at risk for aspergillosis. β(1-3)-D-glucan appears to be of primary interest in the diagnosis of Pneumocystis pneumonia. For PCR-based DNA detection, there is a consensus on the exclusive use of a real-time quantitative format and on serum as the preferred clinical sample due to the ease of pre-analytical steps. Detection of DNA and galactomannan in bronchoalveolar lavage raises interpretation challenges regarding contamination, colonization, and confirmed disease. Concurrently, species identification is a critical step for tailoring antifungal therapy. Rapid methods such as MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization-Time of Flight) mass spectrometry and PNA-FISH (Peptide Nucleic Acid Fluorescence in Situ Hybridization) complement existing techniques to accelerate the identification of the most common species. For rare species causing invasive infections, molecular biology methods should be encouraged to achieve the most accurate identification possible, for both epidemiological and therapeutic reasons. (R.A.)