A cassette for performing multiplex PCR is described. The cassette allows for the automated amplification and detection of multiple nucleic acid targets while limiting contamination. The device facilitates a two-amplification, two-primer PCR protocol which results in highly specific, highly sensitive and semi-quantitative amplification of multiple nucleic acid targets. The cassette contains a cavity, a base with a plurality of chambers, a movable pipette for the transfer of reagents and a detection area. The cassettes are single use, disposable devices which may be loaded with reagents needed for the detection of multiple targets. The cassettes may be used in a hospital or clinical setting to quickly screen clinical samples and detect the presence of infectious agents.