Cleaning is an important factor in the reprocessing of hollow medical instruments. Inadequate cleaning disturbs the disinfection and sterilization process and increases the risk of cross-contamination. An automated washer-disinfector is often used for cleaning medical instruments, by using fluid flow. fluid flow induces shear stress at the wall of medical instruments and is able to detach contamination from the surface. However, there is a lack of studies on the effect of flow rate on the cleaning performance. Also in the ISO standards, no flow requirements can be found to remove contamination. In this study, the relationship between the flow rate and removed mass fraction at different soaking times is investigated to get more insight in the effect of fluid flow on the cleaning performance. The results in this study show that, for smooth tubes with a diameter of 9 mm, the removed mass fraction increases for flow rates up to 7.1 L/min where after the removed mass fraction stagnates. An ANOVA test was performed in combination with a Tukey HSD multiple comparison test to determine significant effects. There is a significant difference in the mass fraction removed, by applying different flow rates (F = 88.24, p = 9.49*10^-33) and different soaking times (F = 15.35, p = 2.8*10^-6), with F as the test statistic from the F-test and p as the p-value. The Tukey HSD test shows significant difference comparing flow rates greater than 5.9 L/min with flow rates smaller or equal to 5.1 L/min. For cleaning with 7.1 L/min, 5.9 L/min or 8.0 L/min no significant differences in the results are found. Furthermore, no significant differences in the cleaning performance of flushing with 3.5 L/min compared to lower flow rates is found. Moreover, this study shows that there is a significant difference between soaking and no soaking. Comparing 5 minutes and 10 minutes soaking no difference are found. This study shows the effect of flow rate on the cleaning performance and it can be concluded that for adequate cleaning of hollow medical instruments the shear stress induced by the flow rate should be taken into account. The results in this study can be used as ground truth to compare to the cleaning performance of different complex geometries with each other. Furthermore, with the method described in this article the effect of more cleaning parameters could be investigated.