Complement activation is involved in the initiation of inflammation and antibody-mediated demyelination in experimental autoimmune encephalomyelitis (EAE). We investigated the role of MAC in apoptosis in myelin-induced EAE in complement C5-deficient (C5-d) and C5-sufficient (C5-s) mice. The number of apoptotic cells assessed by TUNEL assay was significantly increased in C5-d mice during clinical recovery as compared with C5-s mice. Most of the apoptotic cells were lymphocytes, monocytes, and oligodendrocytes. DNA microarray was performed using total RNA extracted from spinal cords. Genes expressed higher in C5-s included members of the caspase (caspase 6, 7), TNF and TNFR families (CD27, FasL, lymphotoxin-beta R) and survivin. These results indicate that C5 and possibly MAC may be required for the limitation of inflammatory response within the central nervous system.