Molecular testing is a promising approach to differential diagnostics and especially to prognostication of uveal melanoma (UM). We have tested a complex biomarker panel that included pathology and a number of cytogenetic and molecular markers on a series of 58 UM samples as a part of a prospective clinical study. Testing of all biomarkers has proved feasible on both FFPE and FNA samples. Molecular verification of UM diagnosis via mutation analysis demonstrated very high sensitivity. Cytogenetic and molecular genetic classifications gave discordant results in most samples from our series; prognostic significance of this discrepancy is yet to be elucidated through final data analysis of this and other prospective studies.