Background: The prothrombin time (PT), also called thromboplastin time (“Quick”), is usually measured using citrated plasma from venous blood. Recently, portable coagulation monitors have been developed, which measure PT using non-anticoagulant capillary whole blood from a finger stick. In the present study, we compared the International Normalized Ratio (INR) of the standard laboratory method (INRven) with the newly developed reagent PT N for the CoaguChek® Pro portable monitor (INRcap) in various patient groups: healthy individuals, patients with oral anticoagulation and patients with a deficiency of coagulation factor V, factor VII or factor X, respectively. Methods: One hundred and fifty-five patients were included in this prospective open comparison study. Capillary PT was measured with the portable coagulation monitor CoaguChek® Pro using the new disposable cartridge PT N (containing rabbit brain thromboplastin). In comparison, PT was measured using citrated venous plasma and the reagent Innovin® on the coagulation analyzer STA-R®. Results: We found a correlation coefficient of 0.85 between capillary and venous INR values among the 100 patients with oral anticoagulation. The slope of the regression line was 1.4 and the y-intercept is −0.65. Agreement between both methods was found to be 80% (95% CI: 72–88%) and the standard-agreement was 85% (95% CI: 78–92%). Among the 30 healthy subjects, the individual differences between INRven and INRcap were in 4 cases 0, in 21 cases 0.1 and in 5 cases 0.2. Conclusion: The new test cartridge PT N was found to be a valuable tool for measuring PT among healthy subjects. However, among patients with oral anticoagulation, agreement between INRcap measured with the new cartridge PT N and INRven was only moderate. Our results show that improvements are necessary for a more valuable measurement of capillary PT with portable coagulation monitors.