Objective The aim of this study from the European Network for the Investigation of Gender Incongruence is to investigate the status of all individuals who had applied for gender confirming interventions from 2007 to 2009, irrespective of whether they received treatment. The current article describes the study protocol, the effect of medical treatment on gender dysphoria and body image, and the predictive value of (pre)treatment factors on posttreatment outcomes. Methods Data were collected on medical interventions, transition status, gender dysphoria (Utrecht Gender Dysphoria Scale), and body image (Body Image Scale for transsexuals). In total, 201 people participated in the study (37% of the original cohort). Results At follow-up, 29 participants (14%) did not receive medical interventions, 36 hormones only (18%), and 136 hormones and surgery (68%). Most transwomen had undergone genital surgery, and most transmen chest surgery. Overall, the levels of gender dysphoria and body dissatisfaction were significantly lower at follow-up compared with clinical entry. Satisfaction with therapy responsive and unresponsive body characteristics both improved. High dissatisfaction at admission and lower psychological functioning at follow-up were associated with persistent body dissatisfaction. Conclusions Hormone-based interventions and surgery were followed by improvements in body satisfaction. The level of psychological symptoms and the degree of body satisfaction at baseline were significantly associated with body satisfaction at follow-up.