OBJECTIVES: Controlling pharmaceutical costs has been the subject of research and analysis in many studies in health economics which have shown that the chronic conditions of patients are an important factor. The present work models pharmaceutical expenditure by different health districts and gender according to the characteristics of chronic conditions. METHODS: An analysis was made of pharmaceutical expenditure between November 2008 and October 2009 of four health districts of the Autonomous Valencian Government, with an assigned population of 625,246. Those who had followed treatments for chronic conditions were identified associating the pharmaceutical groups (ATC codes) with 24 chronic conditions, according to electronic prescription data. Multivariate regression analysis was used, where the pharmaceutical expenditure in primary health care was explained through the gender, pharmaceutical co-payment status and the number of chronic conditions, varying from 1 to 8 or more. RESULTS: The percentage of patients with chronic conditions obtained was of 27.82%, who constituted 58.2% of the total pharmaceutical cost. Pharmaceutical co-payment status was excluded from the model due to its high correlation with the number of chronic conditions. The goodness of fit obtained for explaining the expenditure of the whole population was of 57.2%. The models obtained by health district explained between 56.5 and 60.6%, improving in the models obtained solely for the male population, where they reached 62% for one of the districts studied. Men’s pharmaceutical expenditure was the 68.31% of women’s.  However, the number of chronic conditions has a greater impact on men’s pharmaceutical expenditure than women’s. CONCLUSIONS: Although for the whole population the proposed model explained the 57.2% of the pharmaceutical expenditure, differences can be observed between models obtained for each district or for gender. These models may be more suitable than the general model for cost management and establishing incentives for general practitioners in the different districts.