We describe the case of a man in his 40 s with aggressive multiple sclerosis (MS) who received autologous haematopoietic stem cell transplantation (AHSCT) and subsequently developed probable, if not definite, Chronic Inflammatory Demyelinating Polyradiculoneuropathy (CIDP) and haematological complications. Autoimmune conditions occurring as a side effect of allogenic transplantations are well known in the context of haematological malignancies, but only rarely reported for autologous transplantations. Our case demonstrates that although AHSCT may be effective for suppressing MS inflammatory activity, the profound changes to the immune repertoire may lead to other clinically relevant autoimmune phenomena. A careful benefit-risk evaluation should be conducted in all cases where AHSCT is considered.