The roles of molecular techniques in ocular pathology include: a) aiding the understanding of disease pathogenesis; b) establishing diagnoses; c) predicting prognosis; d) predicting therapy response; and e) detecting residual disease. Examples of recent developments in molecular pathology include better understanding of the sonic hedgehog pathway in BCC; polyomavirus MCPyV in Merkel cell carcinoma; microsatellite instability in sebaceous carcinoma; fusion oncogenes in adenoid cystic carcinoma and mucoepidermoid carcinoma; and A20 gene deletions in conjunctival MALT lymphoma. Molecular techniques, such as IgH-PCR and TCR-PCR, are required regularly for the confirmation of the diagnosis of ocular B- and T-cell lymphomas, respectively. Molecular methods are used for prognostication in uveal melanoma, in combination with the clinical and histomorphological features of these tumours. The presence of monosomy 3 and polysomy 8 was initially detected using FISH but MLPA, aCGH, aSNP and GEP, have been introduced in various ocular oncology centres, providing more detailed information. It is hoped that next generation sequencing will provide potential targets for improved therapies in ocular malignancies.