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Background. According to national epidemiological surveillance records, in Mexico six intestinal infectious diseases (IID) are among the top infectious communicable diseases. However, their incidence, relative importance, and spatial patterns have not been studied in detail. Aims. We examine the epidemiology of IID due to bacteria and protozoa to identify which diseases are most important at two spatial scales, what is their integrated importance locally, and how their incidence correlates with Human Development Index (HDI). Methods. We retrieved yearly number of new cases of eight IID from the national epidemiological morbidity report from 2003 to 2012 at the national level, by state, and to assess such information at a higher spatial resolution we included the municipalities for Mexico City. However, no comparisons were made to other municipalities due to unavailability of data. We compared incidence, obtained the disease-specific relative importance, and inspected spatial patterns for the integrated incidence. Finally, we tested whether HDI is correlated with incidence. Results. We found that, except for two diseases, the relative importance of the other six IID contrasted not only between the national level and Mexico City, but also among states and municipalities in Mexico City. Besides, at both scales the distribution of the incidence showed disease-specific spatial patterns. Finally, there was a lack of consistent correlation between HDI and individual IID at both scales. Conclusion. Our results emphasize the need for local disease-focused selective models for control and prevention of IID. The maps displaying our analyses of epidemiological similarities may be used in orienting such effort. [ABSTRACT FROM AUTHOR]