Identification of fungi is based on macroscopic observations of morphology and microscopic characteristics. These conventional methods are time-consuming and requires expert knowledge. For the past years Matrix-assisted laser desorption ionization-time of flight mass spectrometry has been used for routine bacterial identification in clinical laboratories but not yet in the same extension for fungi. In this study three preanalytic preparation methods for fungi were evaluated in order to shorten the processing time in routine laboratory performance. Clinically relevant strains (n=18) of molds and dermatophytes were cultivated on agar plates and prepared according to the different preparation methods for protein extraction. Each strain was analyzed in quadruplicate by the MALDI Biotyper and the database Filamentous Fungi Library 1.0. The results showed that the genus and species identification rates of the least time-consuming direct extraction method were 33% and 11% respectively. Using the formic acid extraction method, the genus and species identification rates were 83% and 44%, respectively. For the longest sample preparation method, liquid media culturing before formic acid extraction, successfully identified all strains except one, which resulted in an identification rate of 94% and 78% respectively. This study shows that preparing samples in cultured liquid media MADLI-TOF MS effectively identified fungal strains to both genus- and species-level. This method was however too time-consuming and cumbersome to be recommended as a replacement to the conventional method. Future studies should be aimed at expanding the reference library and making the direct extraction method more reproducible in terms of obtaining more reliable identification rates.