Two isoelectric forms of human cystatin C with pI 9.2 and 7.8 have been isolated from urine of patients with different nephrological disorders. Treatment of both forms with alkaline phosphatase revealed that the difference between them is not due to the phosphorylation of some amino-acid residue. Further purification of cystatin C with pI 9.2 by hydrophobic chromatography and N-terminal sequencing showed that it consists predominantly of the full-length form of cystatin C with the N-terminal sequence SSPG-. Cystatin C with pI 7.8 was separated into two peaks. The first represented a pure form truncated by an octapeptide and beginning with the N-terminal sequence LVGG-. The second was a mixture containing 33% of the first peak and 66% of a truncated form with the N-terminal sequence VGGP-. Inhibitory activity of the full-length cystatin C and the pure truncated form has been measured against cathepsins B, H and L and show no significant differences in Ki values. These results further support the proposed mechanism of interaction of cysteine proteinases with their inhibitors cystatins (Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikow, A., Brzin, J., Kos, J. & Turk, V. (1988) EMBO J. 7, 2593-2599).