Background The prescription is one of the factors that influences rational use of medicines. The evaluation of prescribing indicators should contribute to organization of primary health care services. Objective The aim of this study was to evaluate prescribing indicators and associated factors in primary health care in the northeast health district, Belo Horizonte, Brazil. Setting Twenty primary health care units in the Northeast Health District, Belo Horizonte, Brazil. Method The study was cross sectional. Indicators proposed by World Health Organization were used to evaluate rational use of medicines. Main outcome measure Indicators evaluated were average number of medicines per prescription, proportion of medicines with antibiotic, injectable, medicines prescribed by generic name and medicines present in the essential medicines list. Results Three hundred and ninety-nine patients were interviewed. The average number of medicines per prescription was 3.5 (SD 2.2). The proportion of medicines with antibiotic, injectable, medicines prescribed by generic name and medicines present in the essential medicines list was 17.8, 9.8, 94.9, 91.4%, respectively. Patient age ≥60 years was positively associated with number of medicines per prescription (P = 0.00). Conclusion In the northeast health district of Belo Horizonte, the proportion of prescriptions of antibiotics and injections, the adoption of prescribing by generic name and the prescribing of essential medicines were satisfactory in this study considering reference values for these indicators and international scientific literature. However, the mean number of prescribed medicines requires a more in-depth evaluation.