Abstract. In the last decades there has been tremendous research towards the design of fully automatic non-rigid registration schemes. However, apart from the ITK based implementation of Rueckerts B-spline oriented approach, there is a lack of sound publicly available implementations of the modern schemes. The Flexible Image Registration Toolbox (FLIRT) is an attempt to close this gap. It focuses on non-parametric schemes as popularized in the book by Modersitzki [1]. To be successful, it is crucial for any registration scheme to reflect the special properties of the underlying registration problem. Consequently, FLIRT has an open object-oriented architecture which allows for the incorporation of user prescribed building blocks. In its present form, some of the most prominent blocks are already implemented. They may be arranged in a consistent way and cover a wide range of applications. Apart from the flexibility issue, great care has been taken towards fast execution times. The most...