In order to determine the presence of Blastocystis sp. in drinking water at a rural school in Merida, 36 water samples were collected from natural sources that feed the distribution tank and faucets during the months of September, 2008, February and December, 2009, and May, 2010. Samples were processed using the technique proposed by Suresh et al. (2005). All samples were negative. These results suggest that the water was exempt from Blastocystis or that the quantity of viable cysts present in the samples was very low, not permitting reproduction in the culture. This report suggests the importance of using more sensitive techniques to detect low amounts of the organism in drinking water. The study of student water consumption habits at the rural school showed that more than half the population consume boiled water; probably, they are aware that the water source has not been treated for drinking.