Segmentation of positron emission tomography (PET) images is an important objective because accurate measurement of signal from radio-tracer activity in a region of interest is critical for disease treatment and diagnosis. In this study, we present the use of a graph based method for providing robust, accurate, and reliable segmentation of functional volumes on PET images from standardized uptake values (SUVs). We validated the success of the segmentation method on different PET phantoms including ground truth CT simulation, and compared it to two well-known threshold based segmentation methods. Furthermore, we assessed intra-and inter-observer variation in delineation accuracy as well as reproducibility of delineations using real clinical data. Experimental results indicate that the presented segmentation method is superior to the commonly used threshold based methods in terms of accuracy, robustness, repeatability, and computational efficiency.