IlluminaGUI is a graphical user interface implemented for analyzing microarray data from the Illumina BeadChip platform. All key components of a microarray experiment, including quality control, normalization, inference and classification methods are provided in a point and click approach. IlluminaGUI is implemented as a R package based on the R-Tcl/Tk interface and is available for platforms on which R runs including Windows, Mac and Unix-type machines.