FusionViewer is an open source and platform independent viewer that has been specifically designed for PET/CT image display. The combination of PET and CT images offers complementary functional and anatomical information. The application (FusionViewer) facilitates efficient visualization and analysis of PET/CT studies via different viewing modes (linked cursor display, alpha-blend mode, checkerboard mode and split window mode). FusionViewer is implemented in Java and uses the Java OpenGL (JOGL) library and the Insight Segmentation and Registration Toolkit (ITK) library, which make it both a fast and cross-platform application. Its intuitive graphical user interface makes it easy to be used by physicians, radiologists, and research scientists. Several analysis and display tools are already available (navigator, zoom, pan, screen snapshot, ROI, and line measure tool; alpha-blending, checkerboard display, and split window display). Along with PET/CT, several other modalities where co-registered images are often visualized simultaneously have benefited from the use of this software.