The assessment of deviant sexual preference has a long tradition in forensic psychiatry and psychology, as it is one of the strongest predictors for sexual offence recidivism. So far, however, the development of a reliable clinical tool for assessing sexual preference based on brain imaging methods has been unsuccessful. Predicated on the extensive research in basic science, this chapter provides an overview of the current knowledge in measuring sexual arousal and sexual preference in healthy subjects and paraphilic patients using functional brain imaging methods. After a description of the most common methods and experimental designs, studies with healthy subjects are discussed, showing a relatively clear network evoked by sexual arousing stimuli. Furthermore, with respect to the main focus of the chapter, imaging studies on assessing sexual preference are of interest. In the following section, neurobiological models of paraphilia, especially paedophilia, are described, and also studies focusing on structural brain abnormalities in paraphilic patients. Moreover, methods for and results of functional brain imaging studies are discussed that address the question of the underlying neuronal basis of sexual preference in paraphilic subjects. Finally, the potential and limitations of the assessment of (deviant) sexual preference using functional magnetic resonance imaging are critically discussed.