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An automated, flow-through ultrasonic lysis module that is capable of disrupting bacterial spores to increase the DNA available for biodetection is described. The system uses a flow-through chamber that allows for direct injection of the sample without the need for a chemical or enzymatic pretreatment step to disrupt the spore coat before lysis. Lysis of Bacillus subtilis spores, a benign simulant of Bacillus anthracis, is achieved by flowing the sample through a tube whose axis is parallel to the faces of two transducers that deliver 10 W cm−2 to the surface of the tube at 1.4-MHz frequency. Increases in amplifiable DNA were assessed by real-time PCR analysis that showed at least a 25-fold increase in amplifiable DNA after ultrasonic treatment with glass beads, compared with controls with no ultrasonic power applied. The ultrasonic system and integrated fluidics are designed as a module that could be incorporated into multistep, automated sample treatment and detection systems for pathogens.