This cross-sectional study was carried out to investigate the factors which influence risk of anxiety and depression among diabetic and hypertensive patients who refer to family health centers. The Hospital Anxiety and Depression Scale (HADS) was applied for assessment of emotional status of the patients and the Hypertension Compliance Assessment Scale (HCAS) was applied for assessment of adherence to anti-hypertensive therapy. Of a total of 380 patients, 170 had hypertension (HT), 83 had type 2 diabetes mellitus (T2DM), and 127 had both HT and T2DM. According to HADS, 18.7% of the patients had risk of anxiety, 24.7% had risk of depression, and 12.6% had both risk of anxiety and depression. Mean HAD-Anxiety (HADS-A) score and HADS-Depression (HADS-D) score were significantly lower in the patients who had an adequate compliance to medication therapy (5.1 +/- 4.1 and 3.8 +/- 3.4, respectively) compared to the patients who had a low compliance to therapy (7.6 +/- 4.3 and 5.8 +/- 4.0, respectively) according to the Hypertension Compliance Assessment Scale ((2)=15.26, p<0.01 and (2)=13.80, p<0.01). Mean HADS-D score was found significantly lower among the diabetic patients with good glycemic control (3.7 +/- 2.9) compared to the patients with poor glycemic control (4.5 +/- 3.7) ((2)=25.00, p<0.05). Anxiety and depression are among the most frequent disorders as hypertension and diabetes in primary care setting. We revealed that risk of anxiety and/or depression was greater among hypertensive and diabetic patients, consistently with the previous studies. Our study also revealed that this condition negatively affected treatment compliance in hypertensive patients and glycemic control in diabetic patients.