Alicyclobacillus spp. are thermoacidophilic, spore-forming bacteria. Some of which cause spoilage in pasteurized and heat-treated apple juice products through the production of guaiacol. Fourier transform infrared (FT-IR) spectroscopy was used to discriminate between eight Alicyclobacillus strains (WAC, 81-2, Oly#21, 51-1, KF, 1016, 1101, and A-Gala A4) in apple juice. FT-IR vibrational combination bands reflected compositional differences in the cell membranes of Alicyclobacillus strains in the "fingerprint region" at wavenumbers between 1500 and 800 cm(-1). Distinctive segregation among spectral sample clusters of different Alicyclobacillus strains was observed using principal component analysis (PCA). Two closely related strains (1016 and 1101) of Alicyclobacillus acidoterrestris could be distinguished, suggesting that this method can be highly selective. Results of soft independent modeling of class analogy (SIMCA) demonstrated that guaiacol-producing and non-guaiacol producing Alicyclobacillus strains could be differentiated up to 89% of the time. This technique may provide a tool for fruit juice producers to detect Alicyclobacillus rapidly and to monitor and control guaiacol formation.