Axonal loss, demyelination and remyelination progresses following EAE induction. Following tolerisation axonal loss is reduced however still progresses despite the absence of further clinical relapses. Semithin sections from normal, naïve control mice (a, g and m; N = 5), as EAE progresses at day 29 (b, h and n; N = 5), day 58 (c, i and o; N = 5) and 105 days (d, j and p; N = 8), following early (e, k and q; N = 5) and late (f, l and r; N = 5) tolerisation. Panels g-l and m-r are higher magnification images from the red and green boxes respectively in panels a-f. Quantification shows progression of axonal loss (s), with total axonal survival decreasing as EAE progresses, black asterisks (s). Early tolerisation reverses this trend with significant axonal survival (red bar, s) and late tolerisation also has a small but significant effect on axonal survival compared to day 105-crEAE (green bar, s). However, following early tolerisation there is still a significant decrease in axonal survival observed when comparing day 29 to early tolerised mice (s, red bar and asterisks). The majority of those axons surviving at day 29 were normally myelinated (i.e. unaffected) as shown in panel t, yellow segment. Following early tolerisation a significant increase in these remaining normally myelinated axons compared to day 105-crEAE was observed, but a significant decrease compared to day 29 (t, yellow segments) showing a progression on axonal degeneration, even in the absence of the primary immune response. Furthermore remyelination (examples shown by the black arrows in e and f) is significantly increased in early, and to a lesser extent late, tolerised mice by the blue segments (t). Scale bars = 25 μm (a-f) and 5 μm (g-r), significance for data, P < 0.01, one-way ANOVA.