Background: Most studies among Hispanics have focused on individual risk factors of obesity, with less attention on interpersonal, community and environmental determinants. Conducting community based surveys to study these determinants must ensure representativeness of disparate populations. We describe the use of a novel Geographic Information System (GIS)-based population based sampling to minimize selection bias in a rural community based study. Methods: We conducted a community based survey to collect and examine social determinants of health and their association with obesity prevalence among a sample of Hispanics and non-Hispanic whites living in a rural community in the Southeastern United States. To ensure a balanced sample of both ethnic groups, we designed an area stratified random sampling procedure involving three stages: (1) division of the sampling area into non-overlapping strata based on Hispanic household proportion using GIS software; (2) random selection of the designated number of Census blocks from each stratum; and (3) random selection of the designated number of housing units (i.e., survey participants) from each Census block. Results: The proposed sample included 109 Hispanic and 107 non-Hispanic participants to be recruited from 44 Census blocks. The final sample included 106 Hispanic and 111 non-Hispanic participants. The proportion of Hispanic surveys completed per strata matched our proposed distribution: 7% for strata 1, 30% for strata 2, 58% for strata 3 and 83% for strata 4. Conclusion: Utilizing a standardized area based randomized sampling approach allowed us to successfully recruit an ethnically balanced sample while conducting door to door surveys in a rural, community based study. The integration of area based randomized sampling using tools such as GIS in future community-based research should be considered, particularly when trying to reach disparate populations.