The characteristics of tumor cells of primary vitreoretinal lymphoma (PVRL) have not been defined, although researches have shown that most cases are of diffuse large B-cell lymphoma (DLBCL). To determine the subtype and biological characteristics of tumor cells of PVRL, we performed a gene expression profiling analysis. RNA was extracted from the vitreous fluid of seven PVRL patients and from nodal samples of ten DLBCL patients; six of germinal center B-cell (GCB) type and four of activated B-cell (ABC) type determined by Hans' criteria. Six PVRL samples showed gene expression profiles which were similar to each other. The patterns were different from those of the ABC-type nodular DLBCL but relatively close to those of the GCB-type nodular DLBCL. Interestingly, all of the six examined PVRL samples had either MYD88^L265P or mutation in the immunoreceptor tyrosine-based activation motif (ITAM) region of CD79B. Five PVRL patients with similar gene expression profiles were treated with a standardized regimen: a set of intravitreal administration of methotrexate (MTX) followed by six courses of systemic high dose of MTX. As a result, two patients had CD79B mutations and showed early central nervous system (CNS) progression. Patients without CNS progression did not have this mutation. In conclusion, PVRL had unique genetic features: an expression pattern different from ABC-type and relatively close to GCB-type DLBCL. CD79B mutations showed a potential to serve as prognostic markers for CNS progression.