Clonal expansion is a common early event in the development of adult malignancy, but whether this expansion is a precursor to childhood cancers was previously unknown. Phylogenetic analyses were used to study Wilms tumour in order to evaluate its origins. In 61% of cases, premalignant clonal expansions that preceded tumour development were identified in otherwise normal kidney tissue. These expansions were defined by somatic mutations shared between the tumour and normal tissues but not blood cells. Furthermore, hypermethylation of H19, a known driver of Wilms tumour, was observed in 58% of the expansions. Analyses of bilateral tumours suggested that clonal expansions can evolve before the embryological divergence of the left and right kidneys, suggesting that embryonal precursors are present, from which both unilateral and multifocal tumours arise.