The effect of citric or acetic acid on thermal inactivation of Geobacillus stearothermophilus spores is analyzed in this study. The spores were suspended in a tryptone solution or in red beet juice. The tryptone solution (natural pH – 7.1) was acidified with organic acid to the pH values of 6.0, 5.0, 4.0, while the red beet juice (natural pH – 5.8) to the pH values of 5.0 and 4.0. Thermal processing was performed in glass capillaries at the temperature ranging from 115 to 125ºC. It was found that the influence of both acids on the rate of spore inactivation in the tryptone solution was similar, while the type of acid was significant in the red beet juice and the presence of acetic acid had a stronger effect than citric acid. It was confirmed that frequently three-stages were observed in the survivor curves for Geobacillus stearothermophilus present in the media which made the determination of decimal reduction time difficult.