Despite lack of classical lymphatic vessels in the central nervous system (CNS), cells and antigens do reach the CNS‐draining lymph nodes. These lymph nodes are specialized to mediate mucosal immune tolerance, but can also generate T‐ and B‐cell immunity. Their role in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE) therefore remains elusive. We hypothesized that drainage of CNS antigens to the CNS‐draining lymph nodes is vital for the recurrent episodes of CNS inflammation. To test this, we surgically removed the superficial cervical lymph nodes, deep cervical lymph nodes, and the lumbar lymph nodes prior to disease induction in three mouse EAE models, representing acute, chronic, and chronic‐relapsing EAE. Excision of the CNS‐draining lymph nodes in chronic‐relapsing EAE reduced and delayed the relapse burden and EAE pathology within the spinal cord, which suggests initiation of CNS antigen‐specific immune responses within the CNS‐draining lymph nodes. Indeed, superficial cervical lymph nodes from EAE‐affected mice demonstrated proliferation against the immunizing peptide, and the deep cervical lymph nodes, lumbar lymph nodes, and spleen demonstrated additional proliferation against other myelin antigen epitopes. This indicates that intermolecular epitope spreading occurs and that CNS antigen‐specific immune responses are differentially generated within the different CNS‐draining lymphoid organs. Proliferation of splenocytes from lymphadenectomized and sham‐operated mice against the immunizing peptide was similar. These data suggest a role for CNS‐draining lymph nodes in the induction of detrimental immune responses in EAE relapses, and conclusively demonstrate that the tolerance‐inducing capability of cervical lymph nodes is not involved in EAE. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.