Slightly built and not noted for possessing a strong constitution, Morley saw his health deteriorate over the years spent laboring in the Central American jungles under often adverse conditions. Several times, he was incapacitated by recurring bouts of malaria and he had to be hospitalised after separately contracting colitis and then amoebic dysentery the following year. During the 1930s, it also became evident that he had developed cardiac difficulties, which would plague him for the remainder of his life. Nevertheless, although he "detested" the jungle conditions, he persevered in his work with evident enthusiasm.