We report on a genome-wide screen for association with multiple sclerosis (MS) in the German population performed using 6000 microsatellite markers. These markers were typed in four DNA pools consisting of 234 MS patients (cases), 209 unrelated controls, 68 index patients from trio families and their 136 parents (related controls). Stringent analysis identified 11 markers showing apparent evidence for association. Five from regions previously identified in linkage studies and two from the MHC region on chromosome 6p21. These MHC markers are known to be in linkage disequilibrium with HLA class II alleles influencing susceptibility to MS. The identification of these markers serves as an important positive control.