The extent of red blood cell (RBC) aggregation has widely been accepted as a reliable indicator of inflammatory processes. The ability to measure RBC aggregation indexes in capillary blood samples may simplify the application of the test and may bring advantages in its clinical usage as well as application in field studies. This study compared RBC aggregation indexes measured in venous and capillary blood samples using a newly developed capillary tube aggregometer. Although strong correlations between aggregation indexes measured in capillary and venous samples were detected, the indexes measured in venous samples were higher compared to capillary samples, thus indicating a bias. The possible reason for this bias is proposed to be related to the difference in oxygen saturation of venous and capillary samples and therefore altered the light absorption spectrums. Our results indicate that capillary blood samples can be used to estimate RBC aggregation in venous blood samples, however the bias should be taken into account.