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The introduction of novel molecular tools in research and clinical medicine has created a need for more refined information management systems. This article describes the design and implementation of such a new information platform: the Molecular Imaging Portal (MIPortal). The platform was created to organize, archive, and rapidly retrieve large datasets using Web-based browsers as access points. The system has been implemented in a heterogeneous, academic research environment serving Macintosh, Unix, and Microsoft Windows clients and has been shown to be extraordinarily robust and versatile. In addition, it has served as a useful tool for clinical trials and collaborative multi-institutional small-animal imaging research.