Phenols and fatty acids were found to inhibit L-alanine-initiated germination of Bacillus subtilis spores without altering their heat resistance. Inhibitory effect was defined as the concentration necessary to cause 50% inhibition of the germination rate. The quantitative structure-inhibitory activity relationships for 39 phenols and 7 fatty acids were analyzed. The pH dependency of inhibition showed that the nonionized form of the molecule was responsible for inhibition. Hydrophobicity, which was expressed by the partition coefficient or the distribution coefficient of the compounds, was important for inhibition. In addition to hydrophobicity, the electronic effect, which was expressed by the dissociation constant, played a partial role in phenols. The correlation equation of the fatty acids was similar to those of the alcohols and other hydrophobic compounds, which had been reported earlier. That of the phenols, however, appeared to be different, indicating a different and more complex mechanism of inhibition. The type of inhibition by both compounds was mixed rather than competitive or noncompetitive.