Background Endothelial dysfunction is one of the main pathological processes of hypertension. The association of serum pentraxin-3 (PTX3) levels and endothelial dysfunction becomes a more interesting scientific research issue due to high potential of PTX3 as a diagnostic and prognostic biomarker. We aimed to investigate the relationship between serum PTX3 levels and flow-mediated dilation results in patients with dipper and non-dipper hypertension. Methods This study included 90 hypertensive patients were divided into two groups based on 24 hours ambulatory blood pressure monitoring (ABPM): 38 patients with a dipper pattern and 52 patients with non-dipper pattern. Noninvasive evaluation of the endothelial functions was performed using flow-mediated dilation (FMD) method. Results Serum pentraxin-3 levels were higher in patients with non-dipper HT compared to dipper hypertension (P = 0.028). In addition, we found negative correlation between serum PTX3 and FMD basal/FMD hyperemia ratio (r = -0.297, P = 0.05 for FMD basal/FMD hyperemia ratio, respectively). Conclusions Serum PTX3 levels are closely related with the measures of indirect noninvasive evaluation methods (FMD) in both DH and NDH patients.