Objective: To evaluate the influence of organizational structure and technical-management activities on the availability of essential medicines in the primary healthcare. Materials & methods: Cross-sectional, exploratory and evaluative study. The availability was evaluated according to parameters established by the WHO. Results: The average availability of standardized essential medicines was 83.3 and 73.3% for medicines purchased centrally by the Brazilian government. Among the therapeutic groups evaluated, the lowest average availability were for the tuberculostatics (24.1%) and psychotropic/special control medicines (30.3%). Conclusion: The availability of essential medicines was positively influenced by the presence of the pharmacist and by the computerized system deployed, and negatively associated with essential medicines purchased centrally by the federal government, especially in the smaller municipalities.