Objective To clone and characterize Profilin encoding genes in Amaranthus spinosus and to analyze the contribution of different amino acids in isoallergens to allergen antigenicity and tertiary structure. Methods The primers were designed according to the core sequences which were obtained by bioinformatic analysis of the known Profilin amino acid sequences, followed by gene cloning from the Ama- ranthus spinosus cDNA pool and subsequent confirmation by double-digestion, colony PCR and DNA sequen- cing. Antigenicity evaluation and tertiary structural modeling of the encoded protein were accomplished by online software MULTIPRED and SWISS-MODEL, respectively. Results Two panallergenic genes, named as PRF7 and PRF23, were acquired from Amaranthus spinosus. Sequence and structure analysis demonstra- ted that there was some discrepancy in tertiary structures of the encoded proteins, besides distinct difference in their amino acid sequences. PRF7 exhibited high homology with panallergen Profilins Q64LH0, with the identities 98%, whereas the homology of PRF23 and Q9XF42 (apple allergen) was 81%. Q64LH0 and PRF23 were modeled as 3nulA (Q42449) and lg5uB (Q9LE18), respectively. PRF23 exhibited distinct0 three dimensional structural difference in certain fragments compared with Q64LH0 and other Profilins. Though the average values of antigenicity displayed no difference between Q64LH0 and PRF23 on whole se- quences, the antigenicity of PRF23 on certain fragments was obviously lower than that of Q64LHO because of the alteration of some amino acids with different characters, implying the cause of lower incidence of hay fe- ver in South China than in North China. Conclusion Based on sequence analysis, antigenicity evaluation and tertiary structural modeling for Q64LH0 and PRF23, we obtained lots of useful information about the contribution of different amino acids to antigenicity and protein structures, thus would facilitate allergen ge- netic improvement by amino acid replacement.