The Kaiser effect is formally described as the absence of detectable acoustic emission (AE) events until the load imposed on the material exceeds the previous applied level and is usually used to estimate geostress. By focusing on the heterogeneity of rock material, the mechanism of the Kaiser effect under cyclic loading is analyzed based on statistic damage mechanics. Two groups of granite specimens have been cyclically loaded with two different loading paths to verify the theoretical results. The heterogeneity of rock is the real reason that causes irrecoverable damage on the Kaiser effect of acoustic emission in cyclic loading. The Kaiser effect reflects the damaged state in rocks rather than the previous stress imposed on it. Applications for using the Kaiser effect to estimate geostress were discussed here. It is shown that the commonly used uniaxial loading method for estimating geostress is not in accor-dance with the theoretical and experimental results. The analysis is of importance to use the Kaiser effect correctly for estimating geostress or in other fields.