Hepatitis A virus (HAV) and hepatitis E virus (HEV) cause most of the global burden of viral hepatitis. Geographical and seasonal patterns contribute to the epidemiological status of infectious diseases. The extent of these features in the setting of HAV and HEV infections has not been analyzed in detail. This point is important in highly endemic countries of both viruses, where the pediatric population is at high risk of contracting these infections. A comparison between the frequency of antibodies to HAV and HEV and viral RNA detection in serum samples from pediatric patients with acute hepatitis from South and West Mexico was performed. All samples were positive for HAV mono-infection, which was most frequently detected in the metropolitan areas during the rainy season in the South (90%) and all year round in the West (42%). No HEV mono-infection was detected in the studied regions. A 58% frequency for HAV/HEV co-infection was found in the West, predominantly in the metropolitan areas during the rainy months. A 10% frequency for co-infection broadly distributed in the South throughout the year was also found. Our findings underscore that the distribution of HAV and HEV infections varies through the year and differs among Mexico's distinct geographical regions.