BACKGROUND Evidence-based diabetes guidelines generally neglect comorbidity, which may interfere with diabetes management. The prevalence of comorbidity described in patients with type 2 diabetes (T2D) shows a wide range depending on the population selected and the comorbid diseases studied. This exploratory study aimed to establish comorbidity rates in an unselected primary-care population of patients with T2D. METHODS This was a cohort study of 714 adult patients with newly diagnosed T2D within the study period (1985-2007) in a practice-based research network in the Netherlands. The main outcome measures were prevalence and incidence density rates of chronic comorbid diseases and disease clusters. All chronic disease episodes registered in the practice-based research network were considered as comorbidities. We categorised comorbidity into 'concordant' (that is, shared aetiology, risk factors, and management plans with diabetes) and 'discordant' comorbidity. Prevalence and incidence density were assessed for both categories of comorbidity. RESULTS The mean observation period was 17.3 years. At the time of diabetes diagnosis, 84.6% of the patients had one or more chronic comorbid disease of 'any type', 70.6% had one or more discordant comorbid disease, and 48.6% and 27.2% had three or more chronic comorbid diseases of 'any type' or of 'discordant only', respectively. A quarter of those without any comorbid disease at the time of their diabetes diagnosis developed at least one comorbid disease in the first year afterwards. Cardiovascular diseases (considered concordant comorbidity) were the most common, but there were also high rates of musculoskeletal and mental disease. Discordant comorbid diseases outnumbered concordant diseases. CONCLUSIONS We found high prevalence and incidence density rates for both concordant and discordant comorbidity. The latter may interfere with diabetes management, thus future research and clinical practice should take discordant comorbidity in patients with T2D into account.