The development of food preferences contributes to a balanced diet, and involves both innate and learnt factors. By associating flavour cues with the reinforcing properties of the food (i.e. postingestive nutrient cues and innately preferred tastes, such as sweetness), animals acquire individual preferences. How the brain codes and guides selection when the subject has to choose between different palatable foods is little understood. To investigate this issue, we trained common marmoset monkeys (Callithrix jacchus) to respond to abstract visual patterns on a touch-sensitive computer screen to gain access to four different flavoured juices. After preferences were stable, animals received excitotoxic lesions of either the amygdala, the orbitofrontal cortex or the medial prefrontal cortex. Neither the orbitofrontal nor the medial prefrontal cortex lesions affected pre-surgery-expressed flavour preferences or the expression of preferences for novel flavours post-surgery. In contrast, amygdala lesions caused a shift in the preferences for juices expressed pre-surgery such that, post-surgery, juices were chosen according to their overall carbohydrate (simple sugars) content or ‘sweetness’. Subsequent tests revealed that amygdala-lesioned animals only expressed juice preferences if they differed in ‘sweetness’. Unlike controls, orbitofrontal cortex-lesioned and medial prefrontal cortex-lesioned animals, they were unable to display preferences between juices matched for ‘sweetness’ i.e. 5% sucrose solutions aromatised with different essential oils. The most parsimonious explanation is that the amygdala contributes to the expression of food preferences based on learnt cues but not those based on an innate preference for sweetness.