Internet-administered cognitive behavioural therapy (ICBT) has been found to be effective for a range of anxiety disorders. However, most studies have focused on one specific primary diagnosis and co-morbidity has not been considered. In primary care settings, patients with anxiety often suffer from more than one psychiatric condition, making it difficult to disseminate ICBT for specific conditions. The aim of this study will be to investigate if ICBT tailored according to symptom profile can be a feasible treatment for primary care patients with anxiety disorders. It is a randomised controlled trial aimed to evaluate the treatment against an active control group. Participants with anxiety disorders and co-morbid conditions (N = 128), will be recruited from a primary care population. The Clinical Outcome in Routine Evaluation (CORE-OM) will serve as the primary outcome measure. Secondary measures include self-reported depression, anxiety, quality of life and loss of production and the use of health care. All assessments will be collected via the Internet and measure points will be baseline, post treatment and 12 months post treatment. This trial will add to the body of knowledge on the effectiveness of ICBT for anxiety disorders in primary care. The trial will also add knowledge on the long term effects of ICBT when delivered for regular clinic patients ClinicalTrials.gov: NCT01390168.