Melanoma of the uvea of the eye and melanoma of the skin share a common cell of origin, but differ substantially in their behaviour and response to chemotherapy. There is increasing evidence that this is related to differences in their molecular phenotype, particularly in relation to the expression of cell cycle-associated proteins. Since many cytotoxic agents act by damaging DNA, resistance is often associated with intact mechanisms which allow the neoplastic cells to arrest their growth while DNA is repaired, or to resist apoptosis in response to detection of DNA damage. p53 is important to these processes, but mutation appears to be a less common event in uveal melanoma than in skin melanoma, probably due to the lack of UV exposure in the uvea. There are also differences in proliferation-associated proteins such as c-myc and cyclin D1. Overexpression of the former molecule is associated with a poor prognosis in skin melanoma, but is associated with a good prognosis in uveal melanoma, although there is considerable genetic heterogeneity within each type. While prognostic studies may therefore be of little relevance to individual patients, they continue to inform our understanding of tumour biology.