As the pace of clinical magnetic resonance (MR) procedures grows, the need for an MR scanner software platform on which developers can rapidly prototype, validate, and produce product applications becomes paramount. A software architecture has been developed for a commercial MR scanner that employs state of the art software technologies including Java, C++, DICOM, XML, and so forth. This system permits graphical (drag and drop) assembly of applications built on simple processing building blocks, including pulse sequences, a user interface, reconstruction and postprocessing, and database control. The application developer (researcher or commercial) can assemble these building blocks to create custom applications. The developer can also write source code directly to create new building blocks and add these to the collection of components, which can be distributed worldwide over the internet. The application software and its components are developed in Java, which assures platform portability across any host computer that supports a Java Virtual Machine. The downloaded executable portion of the application is executed in compiled C++ code, which assures mission-critical real-time execution during fast MR acquisition and data processing on dedicated embedded hardware that supports C or C++. This combination permits flexible and rapid MR application development across virtually any combination of computer configurations and operating systems, and yet it allows for very high performance execution on actual scanner hardware. Applications, including prescan, are inherently real-time enabled and can be aggregated and customized to form “superapplications,” wherein one or more applications work with another to accomplish the clinical objective with a very high transition speed between applications. © 2002 Wiley Periodicals, Inc. Concepts in Magnetic Resonance (Magn Reson Engineering) 15: 216–237, 2002