The external environment directly influences human health. However, what happens inside? This work deals with the effect that the interior thermal variables have on the propagation of respiratory diseases and focused on the relation of the temperature and relative humidity inside social housing in the 1040 parishes of Ecuador and the transmission of influenza. On the one hand, historical weather-related variables were used to simulate and estimate the interior conditions, and thresholds on temperature and humidity were determined. On the other hand, the health-related variable was determined by analyzing the statistics corresponding to the influenza and viral pneumonia in 2009 since that year was critical for these diseases; the data were divided by month for each parish. Finally, the correlation of these variables determines the relative importance of the interior conditions on the respiratory health of its inhabitants. The preliminary results indicate that the places with the lowest temperatures and relative humidity could favor the virus transmission. Also, the analysis indicated that respiratory diseases increase in August and October. In this way, it is clear that social housing projects in Ecuador require a study which guarantees not only energy efficiency and sustainability related issues but also the well-being of their inhabitants.