Background: Traumatised asylum seekers and refugees are clinically considered a complex population. Discussion exists on whether with this population treatment guidelines for post-traumatic stress disorder (PTSD) should be followed and Trauma-Focused Cognitive-Behavioural Therapy (TF-CBT) or Eye Movement Desensitisation and Reprocessing (EMDR) should be applied, or whether a phased model starting with stabilisation is preferable. Some clinicians fear that trauma-focused interventions may lead to unmanageable distress or may be ineffective. While cognitive-behavioural interventions have been found to be effective with traumatised refugees, no studies concerning the efficacy of EMDR with this population have been conducted as yet. Objective: In preparation for a randomised trial comparing EMDR and stabilisation with traumatised refugees, a pilot study with 20 participants was conducted. The objective was to examine feasibility of participation in a randomised trial for this complex population and to examine acceptability and preliminary efficacy of EMDR. Design: Participants were randomly allocated to 11 sessions of either EMDR or stabilisation. Symptoms of PTSD (SCID-I, HTQ), depression and anxiety (HSCL-25), and quality of life (WHOQOL-BREF) were assessed at pre- and post-treatment and 3-month follow-up. Results: Participation of traumatised refugees in the study was found feasible, although issues associated with complex traumatisation led to a high pre-treatment attrition and challenges in assessments. Acceptability of EMDR was found equal to that of stabilisation with a high drop-out for both conditions. No participants dropped out of the EMDR condition because of unmanageable distress. While improvement for EMDR participants was small, EMDR was found to be no less efficacious than stabilisation. Different symptom courses between the two conditions, with EMDR showing some improvement and stabilisation showing some deterioration between pre-treatment and post-treatment, justify the conduct of a full trial. Conclusion: With some adaptations in study design, inclusion of a greater sample is justifiable to determine which treatment is more suitable for this complex population.