Allergenicity prediction of transgenic expressed protein in crops is important. According to FAO/WHO recommendations, potential food allergenicity in GUS, NptII, and OPH was assessed in the databases of SDAP, Farrp, and NCBI, which were established for allergens prediction. Results of Blast or Fasta alignment online with full sequence or 80 aa window indicated that there was no allergenicity for sequence of GUS, NptII, and OPH. However, in OPH one 6 aa segment matched the sequence of profilin in soybeans, wheat or rubber tree, and another 6 aa segment matched the sequence of allergen-related protein in German cockroach. In GUS, one 6 aa segment matched the allergen “Aed a2” in salivary glands of Aedes aegypti. In NptII, one 6 aa segment matched the hemoglobin of Chironomus thummi. These identical segments did not show antigenicity, so it may be false positive for the matches.