Protein AA, the main fibril protein in secondary systemic amyloidosis, is a mixture of protein fragments (subspecies) of different length, probably arising by enzymatic cleavage of a serum precursor, SAA. We have purified amyloid fibril protein AA from a patient with rheumatoid arthritis and secondary amyloidosis with an unusual amyloid distribution in organs. This protein AA contained two major subspecies of which one consisted of 50 amino acid residues shown by complete amino acid sequence analysis. The other major AA subspecies, characterized by N- and C-terminal sequence analysis and amino acid determination of proteolytic peptides, contained 45 amino acid residues. The pI of these AA-variants differed considerably, 8.1 to 5.5, respectively. Several minor protein AA subspecies were also identified, among them one with a blocked N-terminal. The findings indicate that AA proteins of different length are connected to varying AA amyloid syndromes.