Malaria was one of the toughest obstacles the early Zionist settlers were faced with. The disease, which until today still boasts the dubious title of one of the most common causes of death in the world, was widespread in the area, especially in the Jordan Valley, the Jezreel valleys and the coastal plain. The indigenous Arab population had a hard time dealing with the illness, and the areas prone to malaria remained unpopulated, despite the fact that they were particularly fertile. This is why, when Jewish immigrants began arriving in the area in the late 19th century, these were the areas where they were able to buy land from Arab landowners relatively easily. In a sense, the disease was a main factor in influencing the map of the early Zionist settlements.  
The story of the founding of Petach Tikvah is a case in point. The residents of the Arab village that existed there, Umlabes, abandoned it after a malaria epidemic. The landowner sold it to Jewish settlers who founded Petach Tikvah in 1878. But these soon faced the same problem, and they handled it similarly: when another malaria epidemic errupted in the area in 1880, they abandoned the settlement. In 1886 Yehud was founded in the area, but at a safe distance from the source of the epidemic, as a lesson from that first attempt.
The CZA houses documentation – mainly photographs - of the early anti–malaria endeavors. These endeavors consisted mainly of the planting of eucalyptus trees as means of drying wetlands, and the distribution  of quinine to the population – a substance believed to aid prevention of malaria. In addition the CZA has material documenting advanced research concerning malaria and the ways of dealing with the disease, such as the start of pest control campaigns making use of DDT and the draining of the swamps.