The aetiology of pattern-formation in human naevoid skin disease remains unknown. However, it is likely that the majority of previously proposed mechanisms - those that simply rely on passive clonal trafficking in embryogenesis - are incomplete. A more comprehensive explanation for pattern-formation in naevi invokes the principle of self-organization. We define two types of patterning: anatomical and functional. Anatomical patterning is where the abnormal clone is limited to regions of pathologic skin, while functional patterning is where the abnormal clone and pathologic skin are spatially uncorrelated. From a theoretical perspective self-organized naevoid patterns may be either secondary to local interactions between normal and aberrant genotypes or due to the interaction between aberrant genotypes and the presence of normal embryonic patterning cues. The latter possibility suggests the critical observation and analysis of patterns in naevoid skin disease may lead to unique insights into key aspects of early human embryogenesis.