Several studies suggest that gut microbiota may play an important role in allergic diseases. The present trial aims to examine effects of the probiotic Enterococcus faecalis on symptoms of allergic rhinitis in patients. Effects of this probiotic on the immune system have been reported by several studies, but the majority of the previous trials were animal studies. In addition, it is well known that symptoms in allergic rhinitis are prone to exhibit high placebo responses. Moreover, recent studies report that even placebos without deception (open-label placebos) are highly effective in reducing symptoms of allergic rhinitis. Our study design combines both new approaches to assess effects on allergic symptoms in patients. The objective of this study is to compare the effects of a probiotic treatment (E. faecalis) with effects seen by open-label placebo, concealed placebo treatment and no treatment control. A total of 120 patients with allergic rhinitis will be randomly assigned to one of four different groups: a double-blind probiotic/placebo group (groups 1 and 2), an open-label placebo group (group 3) and a no-treatment group (group 4) to control for spontaneous variation of symptoms. The primary outcome is the evaluation of allergic symptoms using the Combined Symptoms Medication Score. Furthermore, health-related quality of life is examined (Rhinitis Quality of Life Questionnaire). Secondary outcomes include a visual analogue scale on allergic burden and a second quality of life questionnaire. This report describes the study design of the randomised controlled trial. The study design was approved by the ethical committee of the UKT Department of Psychosomatic Medicine and Psychotherapy, Tübingen, Germany. The trial is registered at the German Clinical Trials Register (www.drks.de, DRKS00015804). The trial results will be published in peer-reviewed journals and at conferences. German Clinical Trials Register (www.drks.de, DRKS00015804); Pre-results.