Food and Agriculture Organization/World Health Organization (FAO/WHO) recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is F 35% identity over a sliding window of 80 amino acids.  Our objective was to evaluate the false positive and negative rates observed using the FAO/WHO versus conventional FASTA analyses.  Data used as queries against allergen databases and analyzed to assess false positive rates included: 1102 hypothetical corn ORFs; 907 randomly selected proteins; 89 randomly selected corn proteins; and 97 corn seed proteins.  To evaluate false negative rates of both methods: Bet v 1a along with several crossreacting fruit/vegetable allergens and a bean -amylase inhibitor were used as queries.  Both methods were also evaluated for their ability to detect a putative nonallergenic test protein containing a sequence derived from Ara h 1.  FASTA versions 3.3t0 and 3.4t25 were utilized.  Data indicate a conventional FASTA analysis produced fewer false positives and equivalent false negative rates.  Conventional FASTA versus sliding window derived E scores were generally more significant.  Results suggest a conventional FASTA search provides more relevant identity to the query protein and better reflects the functional similarities between proteins.  It is recommended that the conventional FASTA analysis be conducted to compare identities of proteins to allergens.