Many aspects of biodefense research require quantitative growth assessments of the test agent. This study evaluated the BioNanoPore (BNP™) technology to quantitate Bacillus anthracis and Yersinia pestis faster than traditional plate counting methods. The BNP™ technology enabled quantification of B. anthracis and Y. pestis in phosphate-buffered saline and naïve rabbit blood at 6 and 24 h, respectively. After 6 h of growth, counts for B. anthracis ranged from 6·19-6·45 log10 CFU ml−1 on BNP™, while counts after 24 h on tryptic soy agar (TSA) ranged from 6·51-6·58 log10 CFU ml−1. For Y. pestis, counts on BNP™ at 24 h ranged from 6·31-6·41 log10 CFU ml−1 on BNP™ and ranged from 6·44-6·89 log10 CFU ml−1 on TSA at 48 h. This study demonstrates that the BNP™ technology provides a more rapid detection of B. anthracis and Y. pestis, which could aid in the evaluation of potential medical countermeasures and treatments as well as other biological defense applications such as surface sampling or decontamination efficacy.