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Abstract Background Depression and anxiety are common co-morbid health problems in patients with type 2 diabetes. Both depression and anxiety are associated with poor glycaemic control and increased risk of poor vascular outcomes and higher mortality rates. Results of previous studies have shown that in clinical practice, treatment of depression and anxiety is far from optimal as these symptoms are frequently overlooked and undertreated. Methods/Design This randomised controlled trial will examine the effectiveness of a disease management programme treating symptoms of depression and anxiety in primary care patients with Type 2 diabetes. Patients will be randomized on patient level in 1:1 ratio. Random block sizes of 2 and 4 are used. The disease management programme consists of screening, stepped treatment and monitoring of symptoms (n = 80). This will be compared to care as usual (n = 80). Discussion The disease management model for co-morbid depression and anxiety in primary care patients with diabetes is expected to result in reduced symptoms of depression and anxiety, improved quality of life, reduced diabetes specific distress and improved glyceamic control, compared to care as usual. Trial Registration Dutch Trial Register NTR2626