Recent studies reported contrasting results with respect to the presence of anti-myelin protein antibodies in multiple sclerosis (MS) and their relation with disease activity. This may be due to the heterogeneous specificity of autoantibodies in MS and the inability of most methods to detect pathogenically relevant antibodies. Here, myelin particles were used to detect anti-myelin antibodies in the CSF of MS patients. Subsequently, their relation with MRI parameters was evaluated.Anti-myelin IgG antibody reactivity was determined in the CSF of patients with MS (n = 65) and clinically isolated syndrome (CIS, n = 37) using a novel flow cytometry based assay. In addition, the CSF of patients with other neurological diseases (OND, n = 17), inflammatory neurological diseases (IND, n = 33) and controls (n = 22) was tested.Compared with controls, increased anti-myelin IgG antibody reactivity was most frequently found in the CSF of patients with CIS (46%, p = 0.002), relapsing-remitting MS (56%, p<0.001) and secondary progressive MS (55%, p<0.001), together constituting 85% of all positive CSF samples. In contrast, elevated anti-myelin IgG antibody reactivity was present in a minority of IND patients (21%), marginally present in controls (5%) and absent in OND patients (0%). Most strikingly, anti-myelin IgG antibody reactivity was related to the number of T2 lesions (r = 0.31, p = 0.041) and gadolinium enhancing T1 lesions (r = 0.37, p = 0.016) on brain MRI in CIS and relapse onset MS patients.CSF anti-myelin IgG antibodies are promising specific biomarkers in CIS and relapse onset MS and correlate with MR measures of disease activity.