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Congenital melanocytic naevi (CMN) are pigmented birthmarks, known to be associated with an increased risk of neurological abnormalities and malignant melanoma. Current treatments for the cutaneous lesions and complications are limited for severely affected individuals, driving the research within this thesis into the aetiopathogenesis of this condition. The potential offered by studying rare diseases is also relevant to this project, particularly on the background of the rising incidence of melanoma in young people in the UK. The aims of this research were to expand the clinical description of the condition, to look for predisposing genetic alterations in the germline, to identify possible biomarkers for risk of complications and to investigate the lineage of naevus cells. To these ends we studied a large population of affected children to expand the phenotypic associations, investigating facial features, endocrinological status, pigmentary phenotype and growth, we undertook histopathological phenotyping of cutaneous and neurological lesions using immunohistochemistry and electron microscopy and employed array comparative genomic hybridisation and next generation sequencing for screening of germline haplotypes and mutations. Typical facial features were described in the majority of children with CMN, and the term CMN syndrome was proposed to encompass these. Post-natal growth was found to be rapid, leading to significantly increased BMI compared to the current UK population. Skewed anterior pituitary hormone measurements and increased parental thyroid abnormalities were suggestive of central hormonal dysfunction, however hormonal production from the cutaneous lesions could not be excluded. Histological phenotyping inferred that the primary abnormality underlying CMN may affect a population of stem cells, not necessarily destined to be melanocytes. An association between MC1R genotype and presence and severity of CMN was found using a candidate gene approach, and other germline candidates were identified. The results in this thesis have improved our understanding of the clinical and histological phenotype of CMN, and have identified genetic factors involved in the pathogenesis of the condition.