In this paper, we present Microarray Medical Data explorer (Microarray-MD), a novel software system that is able to assist in the exploratory analysis of gene expression microarray data. It implements a combination scheme of multiple Support Vector Machines, which integrates a variety of gene selection criteria and allows for the discrimination of multiple diseases or subtypes of a disease. The system can be trained and automatically tune its parameters with the provision of pathologically characterized gene expression data to its input. Given a set of new, uncharacterized, patient's data as input, it outputs a decision on the type or the subtype of a disease. A graphical user interface provides easy access to the system operations and direct adjustment of its parameters. It has been tested on various publicly available datasets. The overall accuracy it achieves was estimated to exceed 90%.