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This paper forms part of a major health needs assessment research project of small-scale subsistence farming households in three relatively impoverished villages located close to an active volcano (Popocatépetl) in the rural hinterland of the town of Atlixco, Puebla, Mexico. Our overarching research question is: how do housing conditions, the micro-environment of the lot and dwelling, air and water quality, patterns of food preparation and household behaviors impact health and wellbeing in each community? We use a mixed-methods strategy starting with a survey of almost 250 households to generate baseline data on the health status, treatment, and perceptions of health in each of the four communities. Our housing and health assessment also focusses upon the dwelling structure and perceived problems such as damp and pests; the use of rooms and yard space; and on-site environmental sampling of the water and air quality. In addition, we apply an intensive case-study methodology to five purposively selected farming households in order to highlight how different dwelling structures and conditions, room use, lot maintenance and organization, practices of animal husbandry, fertilizer and agrochemical storage, open fire cooking with wood, and other behaviors shape and impact health and wellbeing. Our findings and conclusions emphasize the need for further research to better understand the epidemiology of these and similar communities. We conclude by offering a series of policy actions to mitigate the risks and hazards that we identify, and argue that in these rural communities the intersections between housing, home, and yard management presents hazards and challenges to health outcomes that are more dynamic and more volatile, than those of most urban housing environments. • Health Needs Assessment. • Intensive Case Study Methodology. • Village Communities in Puebla, Micro-environmental impacts upon health. • Air Quality. • Housing and Health Improvement Policies. [ABSTRACT FROM AUTHOR]