Women with chronic medical conditions require careful contraceptive management. The aim of this cross-sectional study in Tehran was to determine the pattern of contraception use by women with diabetes, hypertension or obesity. A sample of 264 women aged 18–53 years old was recruited; 81 (30.7%) had diabetes type 2, 100 (37.9%) were obese/overweight (BMI > 25 kg/m2) and 83 (31.5%) had hypertension. Across all 3 groups, the rate of use of contraceptive methods was significantly different before and after diagnosis. Before diagnosis of disease the most common method was hormonal contraception in all women (55.0%, 71.6% and 78.3% of diabetic, overweight and hypertensive women respectively), whereas after diagnosis coital withdrawal was the most common method in diabetic and obese/overweight women (41.2% and 28.0% respectively) and almost the most common method for hypertensive women (35.4%). Use of safe and modern methods of contraception in women with certain chronic medical conditions was low and needs more attention.