Background: Gender differences in life expectancy result in a higher proportion of women in the older population. This causes a female preponderance among elderly patients with ischaemic stroke. On the other hand, upper age limits are frequently used in clinical trials, in part due to safety reasons and logistical concerns. In this study, we model how applying upper age limits will lead to a gender disparity in stroke trials, favouring the inclusion of men rather than women. Methods: We analyzed a prospective hospital-based stroke registry covering the entire Federal State of Hesse, Germany. All cases with admission between 2003 and 2005 and a final diagnosis of ischaemic stroke (ICD10:I63) were selected. For various upper age limits (70, 75, 80, 85 and 90 years), we calculated the proportion of men and women excluded based on their age when applying the respective age span to the study population. Results: A total of 34,754 patients were analyzed, and 17,748 (51%) hereof were women. Their mean age was 73.6 ± 12.1 years. The women were older than the men (76.8 ± 11.7 years vs. 70.2 ± 11.7 years; p < 0.001). All upper age limits provoked a significant gender disparity by leaving a higher proportion of female than male patients outside the admissible range. In particular, selecting 80 years as the upper age cut-off excluded 19% of all male patients but 44% of all female patients (p < 0.001). Conclusions: Setting an upper age limit for ischaemic stroke trials is likely not to be gender neutral but withholds a higher proportion of female than male patients from study participation. Investigators should be aware of such gender imbalances, which may involuntarily be transferred into routine clinical practice.