objective: to determine whether the allotypes of complement proteins factor b (bf), c2, c4a and c4b could be markers of rheumatic heart disease (rhd) in the brazilian population. methods: forty-nine patients with chronic rhd were studied. the controls included 65 healthy individuals, matched with the patients according to sex, age and ethnical background. bf, c2, c4a and c4b allotypes were studied by standard techniques including western blots for c2 and c4 variants with monoclonal and polyclonal antibodies. results: this study showed a significantly elevated frequency of the rare c4a6 allotype (p=0.03 rr=11.85) and a decrease of c4a3 in the patients when compared to controls. in addition, c4 null and bf and c4 rare allotypes were more frequent in patients than in controls. conclusions: considering that only rhd patients were included, further investigations are necessary in order to clarify whether c4a6 may be a marker of the cardiac form or of the disease itself.