An assay device processing instrument comprises a plurality of processing modules. A transport system transports an assay device to each processing module, the transport system being adapted to transfer the assay device from the transport system to the module to enable the transport system to transport another assay device while the first is processed by the processing module. A control system controls operation of the transport system such that each assay device is transferred between the modules in a predetermined sequence, and such that a number of assay devices can be processed in different modules simultaneously.