Introduction Compared with other medical specialties, there are lower numbers of female trainees and lower rates of flexible working in gastroenterology. This study aims to examine the experience of male and female trainees to understand specialty demographics and the experience of training. Methods Gastroenterology training data were obtained from the British Society of Gastroenterology (BSG) trainee surveys from 2014, 2018 and 2020, and from the Royal College of Physicians Medical Workforce unit between 2011 and 2019. Data on endoscopy measures from 2011 to 2021 were obtained from the Joint Advisory Group (JAG) on gastrointestinal endoscopy, including the JAG Endoscopy training system and the National Endoscopy Database. Data were segregated and compared by gender. Results The percentage of female gastroenterology trainees remains at around 40%, largely unchanged over the previous decade. From the BSG trainee survey, 29.5% of women have flexible working patterns compared with 2.6% of men (p<0.001), which is lower than other medical specialties. Less than half of female trainees felt confident about their job prospects once they qualify. A greater proportion of male than female trainees achieved provisional colonoscopy certification during training (55% vs 45%, p=0.005) and female trainees took longer to certify than male trainees (63 months vs 56 months, p=0.004). The total length of training time from primary medical qualification to consultancy was the same for men and women. Conclusion Changes must be addressed from a national and institutional level to address equitable access to national training programmes and equality of outcome for male and female trainees.