As in other areas of the biological sciences, a decisive move into the genomics era is underway for the study of helminths. As sequencing technologies improve and costs continue to drop, genomes are becoming available and will eventually be taken for granted by parasitologists and drug discovery researchers as being core knowledge for any organism of interest. Within a decade, it is plausible to envision the availability of draft or complete genomes from 100 nematode and platyhelminth species. Helminth genome sequencing offers substantial challenges to assembly and annotation because of size, repeat and gene structure and sequence polymorphisms. Research programmes in parasitology will need to adapt to effectively make use of these genomes and to identify the most promising opportunities for the application of genomic information to the development of control strategies, including anthelmintics. Immediate avenues for the use of genomes include superior description of gene and protein expression and function through microarrays, proteomics and RNA interference.