The causes of Parkinson's disease and amyotrophic lateral sclerosis are still not known, but there is evidence that metal ions can be involved in processes leading to degeneration and atrophy of neurons in the case of these two neurodegenerative disorders. A synchrotron microbeam X-ray fluorescence technique was applied for topographic and quantitative analyses of selected elements on central nervous system tissue. The thin slices of brain were measured on the undulator beamline ID 22 at the European Synchrotron Radiation Facility in Grenoble, France. The polychromatic beam with the dimension of 5 microm x 2 microm (horizontal x vertical) was used in measurements. Tissues of substantia nigra representing Parkinson's disease, amyotrophic lateral sclerosis, and the control case were scanned. The results obtained indicated that accumulation of some elements depends on the case that the substantia nigra represents. Some variability in the elemental distribution for a given case was noticed as well. To investigate if present differences in the elemental accumulation between analyzed cases are statistically significant, multivariate methods were used. Cluster and discriminant analyses confirmed the significance of the differences in elemental accumulation in biological structures representing the examined cases. The methods used let us classify these structures in separate groups and determine elements, which play the greatest role in the differentiation of the biological structures for each case.