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Abstract Background Respiratory disease can impose a significant burden on the health of rural populations. The Saskatchewan Rural Health Study (SRHS) is a new large prospective cohort study of ages 6 and over currently being conducted in farming and non-farming communities to evaluate potential health determinants associated with respiratory outcomes in rural populations. In this article, we describe the rationale and methodology for the adult component. The study is being conducted over 5 years (2009–15) in two phases, baseline and longitudinal. The baseline survey consists of two components, adults and children. The adult component consists of a questionnaire-based evaluation of individual and contextual factors of importance to respiratory health in two sub populations (a Farm Cohort and a Small Town Cohort) of rural families in Saskatchewan Rural Municipalities (RMs). Clinical studies of lung function and allergy tests are being conducted on selected sub-samples of the two cohorts based on the positive response to the last question on the baseline questionnaire: “Would you be willing to be contacted about having breathing and/or allergy tests at a nearby location?”. We adopted existing population health theory to evaluate individual factors, contextual factors, and principal covariates on the outcomes of chronic bronchitis, chronic obstructive pulmonary disease, asthma and obstructive sleep apnea. Findings Of the RMs selected to participate, 32 (89%) out of 36 RMs and 15 (94%) out of 16 small towns within the RMs agreed to participate. Using the mail out survey method developed by Dillman, we obtained completed questionnaires from 4264 households (8261 individuals). We obtained lung function measurements on 1609 adults, allergy skin test information on 1615 adults; both measurements were available on 1549 adults. We observed differences between farm and non-farm rural residents with respect to individual, contextual factors and covariates. Discussion There are differences between farm and non-farm rural residents with respect to individual and contextual factors and other variables of importance. The findings of the SRHS will improve knowledge of respiratory disease etiology, assist in the development and targeting of prevention programs, and in planning health services with farm and small town populations.