Many letters of the alphabet are consistently mapped to specific colours by English-speaking adults, both in the general population and in individuals with grapheme – colour synaesthesia who perceive letters in colour. Such associations may be naturally biased by intrinsic sensory cortical organisation, or may be based in literacy (eg ‘A’ is for ‘apple’, apples are red; therefore A is red). To distinguish these two hypotheses, we tested pre-literate children in three experiments and compared their results to those of literate children (aged 7–9 years) and adults. The results indicate that some colour–letter mappings (O white, X black) are naturally biased by the shape of the letter, whereas others (A red, G green) may be based in literacy. They suggest that sensory cortical organisation initially binds colour to some shapes, and that learning to read can induce additional associations, likely through the influence of higher-order networks as letters take on meaning.