Background Using written submission with formative feedback as a teaching method, the European Society for Paediatric Endocrinology (ESPE) developed an interactive elearning portal for predoctoral and postdoctoral education and training: (http://www.espe-elearning.org). The aim of the study was to evaluate the role of e-learning in the assessment of competencies of paediatric endocrinology fellows. Competencies included as medical knowledge communication skills and knowing what information to give to patients and parents with a difference of sex development about diagnosis and management. Materials and Method Sixty-eight fellows and 32 experts from various countries participated in the study. Fellows answered online multiple-choice and open questions relating to two clinical interactive problem solving cases (case 1: a new-born with congenital adrenal hyperplasia; case 2: a 17-year-old girl with gonadal dysgenesis). Experts provided anonymous feedback online, using responses guidance (standard questions for eliciting a uniform consideration of competence). Results Fifty percent of fellows answered 16 out of 20 questions correctly on their first attempt at questions about the clinical case scenarios. However, experts judged that only 50 % of the necessary elements of questions 1 and 2 (case 1) and question 2 (case 2) were given in these correct answers. The personalized formative feedback to the open questions provided by the two to three experts 'marking' each submission was highly valued by participating fellows. The most frequently cited items relating to cultural, religious and regional aspects of differences of sex development (DSD) management were relating fertility and role of the family. These were listed by 12/32 experts. Fellows did not mention them in their first reply to the open questions but acknowledged their importance in their second reply. Conclusion The ESPE e-learning portal, offering direct interaction between fellow and trainer, is highly valued by both parties, as helpful in developing medical competencies and is therefore a feasible tool for distance learning.