The invention provides methods of assessing the risk of secondary autoimmunity in a patient with a primary autoimmune disease (e.g., MS) following lymphocyte depleting therapy (e.g., anti-CD52 antibody therapy) based on the fraction of a novel cell type termed platelet lineage cells (PLCs) among total cells, and/or the Immature Platelet Fraction (IPF) value, in a biological sample from the patient.