Background. Hypertension has been related to endothelial dysfunction. Patients with refractory hypertension (RH) have a reduced number of endothelial progenitor cells (EPCs). Aim. To evaluate if blood EPC levels relate to endothelium‐dependent vasodilation (ED‐VD) in RH. Methods. We analyzed 29 RH confirmed by 24‐h ambulatory blood pressure monitoring and assessed complete clinical and laboratory evaluation. EPCs were isolated from peripheral mononuclear cells (MNC) by flow cytometry. ED‐VD was determined measuring flow‐mediated dilation (FMD) by venous occlusion plethysmography. Results. Circulating EPCs/105 MNC (median [Q1–Q3]): 23.0 [4.5–53.8]. FMD (median [Q1–Q3]): 211.7 [79.5–365.8]%. Significant correlations with log‐FMD: EPCs (r = 0.469; p = 0.018) and homocysteine (r = −0.414; p = 0.045). There was no collinearity between EPCs and homocysteine. FMD did not correlate with age, gender, office BP, 24‐h systolic blood pressure or 24‐h diastolic blood pressure, laboratory parameters, C‐reactive‐protein, left ventricular‐mass index, dyslipidaemia, smoking habit and statin or angiotensin system blockers treatment. Multiple linear regression analysis showed that after age‐adjustment, EPC (p = 0.027) and homocysteine (p = 0.004) were the only variables that predicted FMD (R = 0.740). After dividing patients according to EPC number, patients in the lower tertile showed a significantly reduced FMD compared with those in the group of the two upper tertiles of EPC: log‐FMD (mean±SD): 4.7±0.9 vs 5.6±0.8, respectively (p = 0.031). Conclusions. ED‐VD independently correlates with circulating EPCs in RH. Homocysteine is also an independent predictor of lower FMD in such patients.