We show that the neurological condition of synaesthesia--which causes fundamental differences in perception and cognition throughout a lifetime--is significantly represented within the childhood population, and that it manifests behavioural markers as young as age 6 years. Synaesthesia gives rise to a merging of cognitive and/or sensory functions (e.g. in grapheme-colour synaesthesia, reading letters triggers coloured visual photisms) and adult synaesthesia is characterized by a fixed pattern of paired associations for each synaesthete (e.g. if a is carmine red, it is always carmine red). We demonstrate that the onset of this systematicity can be detected in young grapheme-colour synaesthetes, but is an acquired trait with a protracted development. We show that grapheme-colour synaesthesia develops in a way that supersedes the cognitive growth of non-synaesthetic children (with both average and superior abilities) in a comparable paired association task. With methodology based on random sampling and behavioural tests of genuineness, we reveal the prevalence of grapheme-colour synaesthesia in children (over 170,000 grapheme-colour synaesthetes ages 0-17 in the UK, and over 930,000 in the US), the progression of the condition in longitudinal testing, and the developmental differences between synaesthetes and non-synaesthetes in matched tasks. We tested 615 children age 6-7 years from 21 primary schools in the UK. Each child was individually assessed with a behavioural test for grapheme-colour synaesthesia, which first detects differences between synaesthetes and non-synaesthetes, and then tracks the development of each group across 12 months (from ages 6/7 to 7/8 years). We show that the average UK primary school has 2-3 grapheme-colour synaesthetes at any time (and the average US primary school has five) and that synaesthetic associations (e.g. a = carmine red) develop from chaotic pairings into a system of fixed, consistent cogno-sensory responses over time. Our study represents the first assessment of synaesthesia in a randomly sampled childhood population demonstrating the real-time development of the condition. We discuss the complex profile of benefits and costs associated with synaesthesia, and our research calls for a dialogue between researchers, clinicians and educators to highlight the prevalence and characteristics of this unusual condition.