Alzheimer's disease (AD) is the most common cause of senile dementia. In Ecuador, the number of deaths caused by AD increases each year. Epidemiologically, the Ecuadorian population is composed of a mixture of several genetic backgrounds along with environmental factors, that make it unique and ideal for population studies. The main objective of this study was to determine the prevalence of Cystatin C (CST3), Cathepsin D (CTSD) and Manganese superoxide dismutase (MnSOD) amino acid-altering polymorphisms and their influence on the development of AD in the Ecuadorian population.This is a case-control study consisting of 56 patients with AD, from the Department of Neurology at Carlos Andrade Marín Hospital. The control group (n = 55) comprised healthy elderly adults. The inclusion period was from January to August of 2012. Peripheral blood was collected from both groups for DNA extraction, polymerase chain reaction and capillary sequencing.There was a positive association between a CTSD polymorphism (Ala224Val) and the development of AD (odds ratio = 8.1, 95% confidence interval: 0.9-85.7; P < 0.025). However, the 3 other polymorphisms investigated did not show significant associations with AD.Variations in CTSD and MnSOD showed no association with the development of AD, whereas the presence of the Ala224Val polymorphism in CTSD had a positive association with the development of AD.