Nutrition and the incidence of diseases during early life are considered environmental factors that determine people’s height when they become adults. While there is extensive literature focusing on the relationship between physical growth, general mortality and infant mortality rates, few studies analyse the impact of certain disease groups on the final height of historical populations. Using regional mortality rates by causes of death, the main objective of this study is to determine the onset of the disease environment during early life for populations born in Spain between 1916 and 1930, and its relationship with the stature reached at 21 years of age. A population-averaged model is performed on epidemic-infectious, gastrointestinal, and congenital diseases during the gestation period and first year of life. The disease burden in early life had a statistically significant negative effect on adult stature. These results support the premise that an improvement in the disease environment could lead to a greater number of short children surviving and therefore a decrease in the average height.