A new tool in the search for tumour markers is proteomic technology. Proteomics (or protein profiling) is the study of the proteome, the protein complement of the genome. The advantage of this technique in comparison with genomics is that the actual protein production can be measured. Gene microarrays determine levels of mRNA but do not necessarily predict the level of the corresponding proteins in a cell. In this study, we evaluated the use of proteomics in the aqueous humour of uveal melanoma patients compared with control patients using the surface-enhanced laser desorption ionization time-of-flight technique. The protein mass spectra of aqueous humours from 24 uveal melanoma eyes were compared with 24 control eyes using a strong anion exchange surface protein chip array. On the basis of two proteins (4543.43 and 6853.30 kDa), the aqueous humour of melanoma eyes and control eyes could be distinguished in 89% of cases. Therefore, proteomic evaluation might be helpful in finding diagnostic markers for uveal melanoma patients.