The efficacy of microbial inactivation techniques is currently tested using time-consuming and labor-intensive plate count methods, which are the principal rate-limiting steps in developing inactivation kinetic parameters for alternative food processing technologies. Fourier transform infrared (FT-IR) spectroscopy combined with multivariate analysis was used to quantify viable spores and identify some biochemical changes in samples treated by autoclaving, pressure-assisted thermal processing (PATP), and thermal processing (TP). Spore suspensions (∼109 CFU/mL) of Bacillus amyloliquefaciens TMW 2.479 Fad 82, B. amyloliquefaciens TMW 2.482 Fad 11/2, B. sphaericus NZ 14, B. amyloliquefaciens ATCC 49764, and Clostridium tyrobutyricum ATCC 25755 were treated by PATP (121°C and 700 MPa) for 0, 10, 20, and 30 s and by TP (121°C) for 0, 10, 20, and 30 s. The concentrations of spores in treated samples were determined by plating (reference method). Models developed using partial least-squares regression (PLSR) for predicting spore levels in treated samples had correlation coefficients (r) of >0.99 and standard errors of cross-validation ranging between 100.2 and 100.5 CFU/mL. Changes in dipicolinic acid (DPA) and secondary structure of proteins were found to occur during inactivation of spores by PATP and TP. FT-IR spectroscopy could rapidly estimate viable bacterial spore levels in PATP- and TP-treated spore suspensions, providing an accurate analytical tool for monitoring the efficacy of sterilization techniques in inactivating spore-forming microorganisms. © 2006 American Chemical Society.