Women make up 15% of the total number of practicing gastroenterology (GI) physicians in the US. Despite this disparity, only 33% of the current GI fellows are female. Increasing female GIs is a major goal of all four GI societies. It is known that gender disparity exists in the field of gastroenterology, and women are underrepresented in the leadership ranks and trainee level at academic programs. Whether an increase in female leadership in academic medicine is associated with an increase in female program directors and trainees is unknown. The aim of this study was to assess this relationship in GI. Data were collected via a standardized protocol from all 173 US gastroenterology fellowship programs up until October 2018 from program websites and supplemented by online surveys completed by program coordinators. Any missing information was collected by calling the program coordinators. Data were collected on gender and academic rank of the program director, associate program director, division chief, chair of medicine, program size, academic center affiliation, number, and academic rank of female faculty and geographic region. The association was assessed using a Chi-square test or independent samples t test. In leadership positions, men were listed as comprising 86% of chairs, 82% of division chiefs, 76% of program directors and 63% of associate program directors. Forty-three percent of programs did not have female representation at any leadership level. The presence of a female program director or female associate program director was associated with an increase in the number of female fellows (4.03 vs 3.20; p = 0.076; 4.26 vs 3.36; p = 0.041), respectively. Overall, the presence of a female in any leadership position led to an increase in the number of female fellows (4.04 females vs 2.87 females; p = 0.007) enrolled in a program. If a GI division chief was male, the program director was more likely to be male as well (81% male vs. 18.8% female). Conversely, having a female division chief was likely to lead to a more equitable program director representation, 54% female to 48% male (p value < 0.0001, OR 5.03 95% CI 2.04-12.3). Furthermore, if either the internal medicine department chair or GI chief was female, the proportion of female program directors increased to 41% as compared to 19% if both were male (p value < 0.0001, OR 2.99 95% CI 1.34-6.6). Women are significantly underrepresented in the number of practicing gastroenterologists, at all levels of leadership in GI fellowship programs, and at the fellow level. Increasing the number of women in fellowship leadership positions is associated with an increase in female program directors and trainees. Per our knowledge, this is the first study to examine the relationship between female leadership in fellowship programs and the gender of trainees. Increasing female representation in leadership positions would not only address current gender disparity, but it may also increase the number of female future GI trainees.