The completion of genome sequences of pathogenic bacteria and the completion of humangenome project has provided lot amount of data that can be utilized to design vaccines and drug targets.One of the recently adopting strategies for drug designing is based on comparative genomics approach,in which the subtraction dataset between the host and the pathogen genome provides information for aset of genes that are likely to be essential to the pathogen but absent in the host. This approach hasbeen used to identify vaccine and drug targets of Pseudomonas aeruginosa and Helicobacter pylori. Wehave used the same approach to identify the vaccine and drug targets of Clostridium botulinum F strain.Our analysis has revealed that out of 3631 coding sequences of the pathogen, 446 represent essentialgenes that have no human homolog. We have further analyzed these 446 genes by the proteinsequence database to list some 96 genes whose products are possibly exposed on the pathogensurface. This preliminary work reported here identifies a small subset of the Clostridium botulinum Fstrain proteome that might be investigated further for identifying potential drug and vaccine targets inthis pathogen.