In this study, we investigate the basis of T cell recognition of myelin that governs the progression from acute symptoms into disease remission, relapse and chronic progression in a secondary progressive model of demyelinating disease. Until now, the frequency and affinity of myelin-reactive CD4 T cells that elicit relapsing-remitting disease have not been quantified. The micropipette adhesion frequency assay was used to obtain a sensitive and physiologically relevant two-dimensional measurement of frequency and TCR affinity for myelin, as the inherent low affinity does not allow the use of specific-peptide:MHC-II tetramers for this purpose. We found the highest affinity and frequency of polyclonal myelin oligodendrocyte glycoprotein (MOG)-reactive cells infiltrate the CNS during acute disease, while affinities during remission, relapse and chronic disease are not significantly different from each other. Frequency analysis revealed that the vast majority of CNS-infiltrating CD4 T cells are MOG-reactive at all time points demonstrating epitope spread is not a predominant factor for disease progression. Further, time points at which mice were symptomatic were characterized by an infiltration of Th17 cells in the CNS while symptom remission showed an enrichment of cells producing IFN-γ. Also, the ratio of regulatory T cells to Foxp3- CD4 T cells was significantly higher in the CNS at remission than during acute disease. The results of this study indicate that a high frequency of T cells specific for a single myelin antigen, rather than increased TCR affinity or epitope spread, govern the transition from acute symptoms through remission, relapse and chronic disease states.