Acute diarrhoea diseases (ADDs) are one of the major health problems in Aguascalientes, Mexico. Due to the risk of significant increases of ADDs in the hot season, it has been necessary to determine the weather conditions that might lead to escalating ADD events. The effects of El Niño and La Niña phenomena on the morbidity rate of ADD (MRADD) in the State of Aguascalientes were determined during the period of 2000–2010. The MRADD was calculated from cases reported by the State Health Department. The Oceanic Niño Index (ONI) was obtained from the US National Oceanic and Atmospheric Administration. The impact of El Niño and La Niña on the MRADD was determined using the Pearson correlation coefficient and analysis of variance (ANOVA). The results gave a significant inverse correlation between El Niño phenomenon and MRADD (r = −0.55, P = 0.001), but a correlation was not observed on the La Niña phenomenon (r = −0.022, P = 0.888). Field data showed significant inverse influence of El Niño on MRADD for the years 2000–2010.