Abstract: Disclosed is a microassay testing system, including a microfluidic cartridge and a compact microprocessor-controlled instrument for fluorometric assays in liquid samples, the cartridge having integrated process controls and positive and negative assay controls. The instrument has a scanning detector head incorporating multiple optical channels. In a preferred configuration, the assay is validated using dual channel optics for monitoring a first fluorophore associated with a target analyte and a second fluorophore associated with a process control. Integrated positive and negative assay controls provide enhanced assay validation capabilities and facilitate analysis of test results. Applications include molecular biological assays based on PCR amplification of target nucleic acids and fluorometric assays in general.