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 computationally intensive part, the solution of the underlying linear systems, is implemented by state-of-the-art solution techniques. The FLIRT package is publicly available, it comes with a user guide and a collection of example problems. It is the purpose of this note, to describe some of the features of the toolbox.