Objective: This article reviews recent advances in filarial parasite genomics and opportunities for new antifilarial drug research. Methods and results: Genomic approach to filarial parasites provides new prospects for target validation. Comparative genomics filters enable us to select filarial parasite-specific gene products of interest. Functional genomics filters allow the selection of gene products essential for pathogen survival. The validated targets could be prioritized and categorized by informatics methods and manual curation. Conclusion: Lymphatic filariasis and onchocerciasis can be eliminated by either sterilizing or killing adult worms. It is most advantageous to target Wolbachia species for developing new drugs. Functional genomic approaches using microarrays, proteomics, and model organisms, have significantly expanded options for researchers. The genomic-based approach is promising for anti-filarial drug discovery in the future.