High-throughput sequencing and computer technologies have become instrumental for systems biological investigations of pathogens. Importantly, studies of genomes and transcriptomes give insights into the “molecular landscapes” in parasites, which is a significant step toward understanding their biology, interactions with their hosts and the diseases that they cause. This talk gives a brief background on NTDs and their impact, reports on recent progress in the genomics of selected helminths and emphasizes some prospects that such systems biological explorations offer for the development of new interventions to combat NTDs and other infectious diseases.