Beak and feather disease virus (BFDV, species Circovirus parrot) is the causative agent of psittacine beak and feather disease (PBFD), characterised primary by death of nestlings, feather loss and presumed immunosuppression in parrots worldwide. BFDV shows marked genetic heterogeneity, particularly in the open reading frame 2 (ORF2) encoding the capsid protein (Cap), but the impact of this diversity on antibody recognition has not been systematically assessed. In this study, we used seven recombinant Cap proteins derived from ORF2 variants selected to reflect the diversity of BFDV strains circulating in psittacine birds. N-terminally truncated, codon-optimised cap gene constructs were expressed in Escherichia coli and tested by semi-quantitative Western blot and indirect ELISA using sera from eight naturally infected, BFDV PCR-positive psittacine birds. Both assays revealed clear antigen-serum dependent differences in reactivity, with several sera failing to produce detectable signals against some Cap variants under the conditions used. These findings provide experimental evidence that amino-acid variation in Cap can be associated with distinct antibody binding patterns in naturally infected birds. The observed heterogeneity in antigen recognition has direct implications for natural infections with BFDV, for the design and interpretation of BFDV serological assays and should be considered in future development of Cap-based vaccines.