Magnetization transfer and T2 relaxation data were obtained for five white and six gray matter brain structures from 10 normal volunteers and 9 multiple sclerosis patients. Thirty MS lesions were also analyzed. Magnetization transfer ratios and myelin water percentages were compared. Both techniques showed a significant difference between the average of white and gray matter of the normal volunteers as well as the average of normal-appearing white matter and gray matter of the multiple sclerosis patients. The average magnetization transfer ratio and myelin water percentage for lesions were significantly lower than those of normal-appearing white matter. Myelin water percentages and magnetization transfer ratios were uncorrelated in white and gray matter but showed a small (R = 0.5, P = 0.005) but significant correlation in multiple sclerosis lesions. In summary, the myelin water percentage and the magnetization transfer ratio provide quantifiable but largely independent measures of multiple sclerosis lesion pathology.