Isolation of high-quality nucleic acids of microorganism is essential for the molecular testing of biological warfare agents (BAs). In this study, we evaluated three commercially available nucleic acid extraction kits, IT1-2-3^TM (IT), Bio Bulwark^TM pretreatment reagent kit (BB) and MORA EXTRACT (ME), using spores of Bacillus subtilis as a model of Bacillus anthracis . The extraction efficiencies of genomic DNA using IT and BB were approximately 10% and 30%, respectively. The ratio of absorbance (260 nm/280 nm) of each extracted sample showed from 1.7 to 2.0, and indicated that the purity of extracted DNA using these kits was sufficient for the molecular testing. BB could inactivate more than 5×10⁷ spores at the beads beating process. While surviving spores were detected after the beads beating process of IT, and the residual spores might be captured in a spin column filter. Although these kits are enabled for the extraction of nucleic acids of BAs with easy handling, the efficiency of extraction and efficacy of inactivation of BAs are different. So it is important to understand the characteristics of each kit before use.