Laboratory identification of carbapenemase-producing clinical isolates is crucial to limit the spread of the bacteria. In this study, we shall first develop the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) assay in automatic identification of carbapenemase producers. A total of 143 well-characterized isolates were studied. After an incubation of bacteria with meropenem trihydrate, the mixture was centrifuged and the supernatant analyzed by MALDI-TOF MS. A genetic algorithm model with ClinProTools software was built using spectra of 43 carbapenemase-positive isolates and 40 carbapenemase-negative isolates after 2 h of incubation. This model was externally validated using 60 test isolates. All spectra of supernatants of the carbapenemase-negative isolates showed peak profiles comparable to that of pure meropenem (m/z 384.159, 406.140, and 428.122 of its two sodium salt variants) regardless of the incubation time tested. For the carbapenemase-positive isolates, the specific peak for meropenem at m/z 384.159 disappeared during the incubation time, two products of meropenem degradation were identified with m/z 358.18 (the decarboxylated product) and 380.161 (sodium salt of the decarboxylated product), and other degradation products were observed (native molecule with disrupted amide bond with m/z 402.169, three sodium salt variants with m/z 424.151, 446.133, and 468.115). Sixty test isolates were 100 % correctly classified as carbapenemase positive and carbapenemase negative with the genetic algorithm model. MALDI-TOF MS coupled with ClinProTools is capable of rapidly, accurately, and automatically identifying carbapenemase producers.