This article discusses the use of a dual monochromator based microplate spectrofluorometer in the analysis of molecular beacons used to monitor PCR reactions. The SPECTRAmax GEMINI spectrofluorometer is the first such instrument that incorporates Excitation and Emission dual scanning monochromators in its design. This feature gives the sensitivity that is required to analyse PCR products and provides the platform to excite and collect emission light from any wavelength pair in the region 250 to 850 nm, directly fit om the PCR plate. Up to 4 wavelength pairs can be selected to analyse up to four probes in a single mixture. In this article we show data from typical targets, and dyes such as TET, FAM and TAMRA. The use of this analytical technology with a 96 or 384 well PCR plate gives the scientist a true high throughput method of monitoring the PCR reaction in their laboratory without the need for more dedicated expensive equipment.