To decide optimally between available options, organisms need to learn the values associated with these options. Reinforcement learning models offer a powerful explanation of how these values are learnt from experience. However, human choices often violate normative principles. We suggest that seemingly counterintuitive decisions may arise as a natural consequence of the learning mechanisms deployed by humans. Here, using fMRI and a novel behavioural task, we show that, when suddenly switched to novel choice contexts, participants choices are incongruent with values learnt by standard learning algorithms. Instead, behaviour is compatible with the decisions of an agent learning how good an option is relative to an option with which it had previously been paired. Striatal activity exhibits the characteristics of a prediction error used to update such relative option values. Our data suggest that choices can be biased by a tendency to learn option values with reference to the available alternatives.