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In this paper, we propose and analyse a mathematical model for the onset and development of autoimmune disease, with particular attention to stochastic effects in the dynamics. Stability analysis yields parameter regions associated with normal cell homeostasis, or sustained periodic oscillations. Variance of these oscillations and the effects of stochastic amplification are also explored. Theoretical results are complemented by experiments, in which experimental autoimmune uveoretinitis (EAU) was induced in B10.RIII and C57BL/6 mice. For