Fast fluid-attenuated inversion-recovery (FLAIR) and proton density/T2-weighted fast spin echo (FSE) brain images with 3-mm slices were acquired monthly for 7 months in 37 multiple sclerosis patients. New and enlarging lesions were counted and compared according to the site of lesions seen with each sequence. In addition, the number of new enhancing lesions seen on gadolinium-enhanced T1-weighted brain magnetic resonance imaging at the same time points was counted. All sequences used 3-mm contiguous axial slices. Overall, 126 new or enlarging lesions were seen on FSE and 135 on fast FLAIR (P = 0.25, Wilcoxon signed ranks test). Regional comparisons revealed significantly more fast FLAIR lesions only in the cortical/subcortical areas. There was a total of 295 new enhancing lesions over the same period -- a gain in the number of 'active lesions' of 234% seen with FSE and 218% with FLAIR. It is concluded that serial thin slice fast FLAIR is only slightly superior to FSE in detecting new and enlarging multiple sclerosis lesions but the difference is not sufficient to recommend that FLAIR should replace FSE in short-term, exploratory trials in MS using monthly scanning. Gadolinium-enhanced imaging is more then twice as sensitive as either FSE or fast FLAIR to new multiple sclerosis lesion activity, and enhancing lesions should provide the primary outcome measure in such studies.