Parasites found in the human gastrointestinal tract can be largely categorized into two groups, protozoa and helminths. The soil-transmitted helminths (Ascaris lumbricoides, hookworm and Trichuris trichiura) are the most prevalent, infecting an estimated one-sixth of the global population. Infection rates are highest in children living in sub-Saharan Africa, followed by Asia and then Latin America and the Caribbean. The current momentum towards global drug delivery for their control is at a historical high through the efforts of numerous initiatives increasingly acting in coordination with donors, governments and local communities. Together, they have delivered enormous quantities of drugs, especially anthelmintics to children through nationwide annual or biannual mass drug administration largely coordinated through schools. However, a much larger and rapidly growing childhood population in these regions remains untreated and suffering from more than one parasite. Mass drug administration has profound potential for control but is not without considerable challenges and concerns. A principal barrier is funding. Stimulating a research and development pipeline, supporting the necessary clinical trials to refine treatment, in addition to procuring and deploying drugs (and sustaining these supply chains), requires substantial funding and resources that do not presently exist. Limited options for chemotherapy raise concerns about drug resistance developing through overuse, however, satisfactory pharmaco-epidemiology and monitoring for drug resistance requires more developed health infrastructures than are generally available. Further, the limited pharmacopeia does not include any effective second-line options if resistance emerges, and the research and development pipeline is severely depressed. Herein, we discuss the major gastrointestinal protozoa and helminths reviewing their impact on child health, changing epidemiology and how this relates to their control.