Background No comparisons have been made of scales estimating cardiovascular mortality and overall cardiovascular morbidity and mortality. The study objectives were to assess the agreement between the Framingham-D'Agostino cardiovascular risk (CVR) scale and the chart currently recommended in Europe (SCORE) with regard to identification of patients with high CVR, and to describe the discrepancies between them and the attendant implications for the treatment of hypertension and hyperlipidaemia. Methods A total of 474 hypertensive patients aged 40–65 years monitored in primary care were enrolled into the study. CVR was assessed using the Framingham-D'Agostino scale, which estimates the overall cardiovascular morbidity and mortality risk, and the SCORE chart, which estimates the cardiovascular mortality risk. Cardiovascular risk was considered to be high for values ≥ 20% and ≥ 5% according to the Framingham-D'Agostino and SCORE charts respectively. Kappa statistics was estimated for agreement in classification of patients with high CVR. The therapeutic recommendations in the 2007 European Guidelines on Cardiovascular Disease Prevention were followed. Results Mean patient age was 54.1 (SD 7.3), and 58.4% were males. A high CVR was found in 17.5% using the SCORE chart (25.3% males, 6.6% females) and in 32.7% using the D'Agostino method (56.9% males, 12,7% females). Kappa coefficient was 0.52, and increased to 0.68 when the high CVR threshold was established at 29% according to D'Agostino. Hypertensive patients with high SCORE and non-high D'Agostino (1.7%) were characterized by an older age, diabetes, and a lower atherogenic index, while the opposite situation (16.9%) was associated to males, hyperlipidaemia, and a higher atherogenic index. Variables with a greater weight in discrepancies were sex and smoking. A 32.0% according to SCORE and 33.5% according to D'Agostino would be candidates to receive antihypertensive treatment, and 15.8% and 27.3% respectively to receive lipid-lowering treatment. Conclusion A moderate to high agreement was found. SCORE may underestimate risk in males with an unfavourable lipid profile, and D'Agostino in diabetics with a lower atherogenic risk. Use of the D'Agostino scale implies treating more patients with lipid-lowering and antihypertensive drugs as compared to SCORE.