In recent decades increase in population growth and urbanization have led to an increase in environmental pollution, which are the main causes of several diseases prevalence. Non-communicable diseases are the most important cause of human death in the world. Cardiovascular diseases are one type of non-communicable diseases. Several studies have shown that urban characteristics such as type and composition of land uses, distance to city center as well as lifestyle-related factors, are the important risk factor to human health. Urban structure is a structural arrangement of different land-uses such as green spaces, residents, recreational area, urban street network and public places. These urban factors influence population health and diseases prevalence, in related to their properties. The purpose of this study was to investigate the relationship between city structure and cardiovascular diseases risk in Isfahan. Isfahan is one of the major cities of Iran where the prevalence of cardiovascular diseases is high due to its characteristics. Cardiology data from Isfahan Cardiovascular Research Institute was collected and separated and mapped in GIS by patients' addresses in 15 Isfahan urban districts. The relationship between the prevalence of cardiovascular diseases and urban and socio-economic parameters such as population density, green space, residential building area, aging, distance from city center and education studied by statistical analysis (Principal Components Analysis, regression tree, analysis of variance, cluster analysis, Nonparametric regression analysis). The results showed the inverserelationshietween distance to city center and the prevalence of cardiovascular diseases, so that with increasing distance to city center of more than 4000 meters, the prevalence of cardiovascular diseases declines sharply. There is also a direct correlation between the aging and cardiovascular diseases risk, so that by increased the aging population rate from 2% to 16%, the prevalence of cardiovascular diseases increased from 1.4% to 2%. On the other hand, the prevalence of cardiovascular diseases decreases with increasing in average of residential building (more than 36 square meters per person). Such relation observed between green space areas (more than 40 square meters per person). The effects of educational variables and population density on the prevalence of cardiovascular diseases aren’t significant. Regarding to the effects of urban structure and it's characteristics on the the prevalence of cardiovascular diseases, considering these variables in urban management and citizens health studies and planning is so important. Keywords : distance from city center, regression tree model, prevalence of cardiovascular diseases.