In this study the retinal transcriptome was investigated during the development of experimental autoimmune uveoretinitis (EAU) in mice. EAU was induced by immunizing B10.RIII mice with human interphotoreceptor retinoid binding protein (hIRBP) 161-180 peptide. Genome-wide transcriptional profiles of EAU (day 7, 14 or 21 after immunization) and of control retinas were generated using DNA-microarrays and bioinformatic data mining. Microglia-associated transcripts were identified. Quantitative real-time polymerase chain reaction was performed to validate the expression of differentially expressed genes. Retinal transcript validation revealed that complement and interferon-related pathways, as well as gene clusters specific for antigen-processing and -presentation, and immunosuppression are involved during the course of the disease. Immunofluorescence analysis confirm that upregulated transcripts in EAU are also expressed by retinal microglia. Furthermore, the heterogenous expression patterns observed in retinal microglia, suggests the presence of different subpopulations of retinal microglia in EAU. This study expands our knowledge of the local immune processes involved in EAU pathology.