In this pilot study 36 patients with anorexia nervosa (AN) will be randomized to either treatment with psychotherapy as usual (TAU) or TAU plus fecal microbiota transplantation (FMT). The transplantation will be performed when refeeding has started. Patients randomized to TAU+FMT will choose either capsules or gastroscopy as source of FMT. One week after FMT gut microbiota will be collected and analyzed and compared with microbiota composition at baseline. The two groups are then followed during psychotherapy to assess whether it is feasible to give FMT during psychotherapy to study the effects on outcome. In addition, this pilot study is aiming at paving the way for performing larger studies to assess whether FMT improves outcome from psychotherapy when given in combination with psychotherapy in patients with AN.