Many chronic diseases follow a course with multiple relapses into peri
ods with severe symptoms alternating with periods of remission; experi
mental allergic encephalomyelitis, the animal model for multiple scler
osis, is an example of such a disease. A finite Markov chain is propos
ed as a model for analyzing sequences of ordinal data from a relapsing
-remitting disease. The proposed model is one in which the state space
is expanded to include information about the relapsing-remitting stat
us as well as the ordinal severity score, and a reparameterization is
suggested that reduces the number of parameters needed to be estimated
. The Markov model allows for a wide range of relapsing-remitting beha
vior, provides an understanding of the stochastic nature of the diseas
e process, and allows for efficient estimation of important characteri
stics of the disease course (such as mean first passage times, occupat
ion times, and steady-state probabilities). These methods are applied
to data from a study of the effect of a treatment (transforming growth
factor-beta(1)) on experimental allergic encephalomyelitis.