Background C. albicans is the most important yeast that caused the infection in humans; the trend of resistance to fluconazole (FLC) was also increased, while the FLC susceptibility by conventional method takes time causing the treatment failure. To investigate FLC susceptibility to C. albicans using MALDI-TOF MS and Real-time PCR for CDR1, CDR2, MDR1 and ERG11, overall, 32 C. albicans strains included 4 reference strains (3 FLC susceptible (S) and 1 FLC resistant (R), 1 spontaneous mutant strain (FLC susceptible-dose dependent, SDD) and 27 clinical strains obtained from 2 Thai University Hospitals were performed FLC susceptibility testing by Sensititre YeastOne and broth microdilution method, FLC resistant expression mechanism by Real-time PCR and the major peak determination by MALDI-TOF MS.Results The change of CDR1 and CDR2 mRNA expression were only significantly observed in SDD and R strains. Using MALDI-TOF MS, the change of mass spectral intensity at range 3376-3382 m/z (major peak) was significantly related to FLC susceptibility as SDD (decreased at 4 µg/ml and increase at 8 µg/ml), S (all increased), and R (all slightly decreased or no change) after incubation for 6 h. All 27 clinical strains showed FLC MIC susceptible (MIC range 0.25-2 µg/ml), no change in CDR1 and CDR2 expression and S major peak type. The FLC resistance C. albicans with CDR1 and CDR2 expression may possibly effect the change of mass spectral intensity at range 3376-3382 m/z. Conclusions The MALDI-TOF MS may be used to simultaneously classify and predict FLC resistant C. albicans strains associated with CDR1 and CDR2 expression. Further studies are essential to clarify the methodology and improve the reliability of this assay for routine diagnosis.