A breath analysis system that includes a handle assembly with an analysis cartridge on an upper end thereof. The handle includes a main body portion with a pressure opening and a pressure transducer therein. The analysis cartridge includes a main body portion with an upper portion that defines a breath chamber, a lower portion that defines a fluid chamber and a filter assembly that is movable between a breath capture position and an analysis position. The filter assembly has an opening defined therethrough. In the breath capture position, the opening partially defines the breath chamber and in the analysis position the opening partially defines the fluid chamber. The system also includes an analysis device with a case, a door, a controller that controls the motor and a fluorescence detection assembly and a rotation assembly positioned in the case interior. The rotation assembly includes a shroud with a funnel portion for receiving the analysis cartridge.
