MultiGeneBlast is an open source tool based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates. MultiGeneBlast can aid in the detection of such multigene parts for synthetic biology projects. A synthetic library of operons can be created based on its output to identify those operons whose function is closest to the one desired by the user. This tool provides the opportunities to identify all homologous genomic regions by combining the results of single BlastP runs on each gene, and sorting genomic regions from any GenBank entry by the number of hits, synteny conservation, and cumulative Blast bit score. Architecture searches can be performed to find any genomic regions with Blast hits to any user-specified combination of amino acid sequences.