This study aimed to analyze possible associations between the Infection Control Structure Score (ICSS), health services, and social characteristics of the municipalities in Brazil. Secondary data from the third cycle 2017-2018 of the Brazilian National Program for Improving Primary Care Access and Quality (PMAQ) was analyzed. Six independent variables - FIRJAN Index of Municipal Development, number of inhabitants, number of family health teams receiving a financial incentive from the federal government, healthcare expenditure per capita, and number of Oral Health Teams modalities 1 and 2 - were included to assess their influence on ICSS, measured for each Brazilian town. Data analysis used the Classification and Regression Tree model performed with IBM SPSS 25. A total of 4,900 municipalities were included, and the mean ICSS was 0.905 (±0.092). A positive relationship was observed between healthcare expenditure per capita, municipal development, and the outcome. Conversely, towns with a higher number of family health teams receiving a financial incentive from the federal government showed lower mean ICSS. The findings suggest that inequalities in the infection control structures exist within the country, and they were related to the health services and social characteristics of the municipalities.