Abstract Background Although a variety of treatment guidelines for Type 2 diabetes patients are available, a majority of patients does not achieve recommended targets. We aimed to characterise Type 2 diabetes patients from Swiss primary care who miss HbA1c treatment goals and to reveal factors associated with the poorly controlled HbA1c level. Methods Cross-sectional study nested within the cluster randomised controlled Chronic Care for Diabetes study. Type 2 diabetes patients with at least one HbA1c measurement ≥7.0 % during the last year were recruited from Swiss primary care. Data assessment included diabetes specific and general clinical measures, treatment factors and patient reported outcomes. Results 326 Type 2 diabetes patients from 30 primary care practices with a mean age 67.1 ± 10.6 years participated in the study. The patients’ findings for HbA1c were 7.7 ± 1.3 %, for systolic blood pressure 139.1 ± 17.6 mmHg, for diastolic blood pressure 80.9 ± 10.5 mmHg and for low density lipoprotein 2.7 ± 1.1. 93.3 % of the patients suffered from at least one comorbidity and were treated with 4.8 ± 2.1 different drugs. No determining factor was significantly related to HbA1c in the multiple analysis, but a significant clustering effect of GPs on HbA1c could be found. Conclusions Within our sample of patients with poorly controlled Type 2 diabetes, no “bullet points” could be pointed out which can be addressed easily by some kind of intervention. Especially within this subgroup of diabetes patients who would benefit the most from appropriate interventions to improve diabetes control, a complex interaction between diabetes control, comorbidities, GPs’ treatment and patients’ health behaviour seems to exist. So far this interaction is only poorly described and understood. Trial registration Current Controlled Trials ISRCTN05947538.