In order to identify the genomic regions that might confer susceptibility to multiple sclerosis (MS) in the Spanish population, we have performed a genome-wide screen for association in patients with MS using pooled DNA from 200 clinical cases and 200 healthy controls. The pools were typed using 5546 microsatellites. The typing was repeated for the most promising 1269 markers after which 191 potentially associated markers were identified. Eleven of these markers map to the MHC region, and 14 to non-MHC regions identified in previous linkage screens. Our results provide support for the presence of multiple coding regions that contain MS susceptibility genes of small or moderate effect.