A holder for PCR sample collection and preparation and method of using which has a buffer container housing removably connected to a plunger housing. A swab attached to an end of a plunger collects a sample of a specimen to be analyzed for biological warfare agents. The swab and plunger are inserted into the plunger housing, a buffer container is positioned inside the buffer container housing and the buffer container housing and plunger housing are attached. A buffer passes through the swab and elutes off the sample and the sample mixes with a reagent. The prepared sample loads into a reaction tube, by a whipping action, for analysis.