Drinking water (DW) can serve as a route for disease transmission if not properly managed. The study assessed the effect of different factors on Escherichia coli quantities in DW in household water storage containers in suburban and rural villages in Laos and Thailand. Higher E. coli concentrations in DW were found in Laos compared to Thailand, especially in households without toilets (in Laos) and in rural rather than in suburban villages. In suburban Laos, house material, storage container types and lack of toilets were significantly associated with E. coli contamination of DW, whereas in rural Laos, corresponding significant factors were rain-fed water, containers with lids and lack of toilets. In suburban Thailand, rain-fed water, storage container types and container cleaning frequency were significantly associated with DW contamination, while house materials, manually collected rainwater and container cleaning frequency were associated with contamination in rural Thailand. Socio-demographic characteristics were less associated with E. coli contamination of DW in this study. Treatment of household stored water (e.g. boiling), regular cleaning of rain jars as well as the provision of household toilets, especially in Laos, can provide barriers against E. coli contamination of DW.