Flavour scientists use a wide range of increasingly sophisticated analytical tools to characterise their samples and assess chemical senses at the receptor level, varying from 'classic' bench instrument techniques to more recent methods of determining the availability of tastants and volatiles at the receptor level, such as mouth swabbing and in-nose atmospheric pressure chemical ionisation mass spectrometry (Taylor et al., 2000). Sensory scientists assess the final perceptual output, for example using panels of trained assessors. Until recently, there has remained a frustrating investigational gap at the interface between these two sciences: flavour input and output scores reported by assessors. This is because the interface occurs at the subject's brain, which has effectively been a 'black box'. Signals from taste, olfactory and somatosensory receptors travel via nerve afferents to primary, secondary and the higher-order brain areas responsible for detecting stimuli and forming associations, decision-making and emotional responses to the flavour experienced. Improved understanding of the neural pathways involved in flavour processing has been facilitated by parallel advances with animal models and human studies. Invasive single-cell recordings and surface electroencephalography (EEG) have facilitated the development of animal models. These studies provide data on cell reactivity to characterise a particular cortical region with millisecond temporal resolution, but they give little detail on how information is processed at several levels. More recently in the past decade, an explosion in the availability and use of non-invasive human brain mapping techniques has allowed serial studies of hierarchical cortical processing in alert healthy human volunteers.Interest in applying brain imaging techniques to study the chemical senses is rapidly growing and to date over 400 studies using different methodologies have been published. The majority of these studies explore the cortical representation of individual sensory attributes of uni-modal stimuli, but there has been recent growth in the study of how the 'cross-modal' integration of sensory inputs in flavour perception is represented in the human brain.This chapter provides a brief outline to human brain anatomy, the cortical pathways used in the experience of taste, aroma and texture and their integration. Functional brain imaging techniques are reviewed, with particular focus on functional magnetic resonance imaging (fMRI) and aspects of experimental design, data acquisition and data processing. This is followed by a brief review of brain imaging studies of the cortical representation of taste and aroma, from early studies investigating the cortical response to pleasant and aversive taste stimuli to recent studies on multi-modal perception and the cortical representation of the oral perception of fat.