Rainwater (RW) is considered an improved source of drinking water (DW) by the WHO and UN agencies tracking progress towards achieving the safe water access target of the Millennium Development Goals. There are, however, a paucity of data on the microbial quality of RW, making uncertain its safety as a DW source. The objective of this work was to evaluate the microbial quality of stored RW collected in a rural village in Thailand using the WHO DW quality guideline value of <1 E. coli/100mL as the basis for safety. In 2011, 59 households in Khon Kaen province, all of which used RW as their primary source of DW, were visited twice, once during dry season and once during rainy season. Observational data related to the physical/sanitary conditions of RW harvesting systems (RWHS) were collected during visits. Sampled containers included each household’s main RW collection tank and the refillable container used to store RW for daily consumption. Samples were assayed for E. coli by the Colisure Quantitray 2000 method and results were scored as present if E. coli was ≥1/100mL. Of all samples processed (collection tank, refillable container), 39% and 82% of households had E. coli present in at least one container during the dry and wet seasons, respectively. E. coli was present in 21% and 66% of RW collection tanks during the dry and wet seasons, respectively. Initial analysis suggests that no single factor related to RWHS setup (roof, pipe, or tank material) had a statistically significant impact on the presence of E. coli in RW collection tanks. These results suggest that stored RW microbiologic quality may be highly seasonal, may not always meet WHO guidelines for safe DW, and that deterioration of the microbiologic quality of stored RW is likely due to a combination of collection and use practices. These results document that the UN Joint Monitoring Program’s use of access to improved water supplies as an indicator of progress towards the MDG safe water target results in overestimation because improved sources, like harvested RW, may be microbiologically unsafe.