Women with polycystic ovary syndrome (PCOS) are at risk for metabolic syndrome, which may be exacerbated by smoking. We hypothesized that smoking worsens androgen levels and the metabolic profile in women with PCOS. PCOS smokers (n = 47) and non-smokers (n = 64) and control smokers (n = 30) and non-smokers (n = 28), aged 18-45 years, underwent anthropomorphic measurements, pelvic ultrasound and blood sampling. Smokers had higher cotinine (801 ± 83 versus <11 nmol/L; smokers versus non-smokers, respectively; p < 0.001) and nicotine levels (37 ± 4 versus <12 µmol/L; p < 0.001). Triglyceride levels were higher in women with PCOS who smoked compared to non-smokers (1.55 ± 0.18 versus 0.95 ± 0.08 mmol/L; p < 0.001), even when adjusted for BMI. Metabolic syndrome was more common in smokers with PCOS compared to non-smokers with PCOS and smokers who were controls (28.6 versus 3.6%; p = 0.02). There were no differences in reproductive parameters including androgen levels. Cotinine (r = 0.3; p < 0.001) and nicotine levels (r = 0.2; p = 0.005) correlated with triglycerides. Nicotine levels also correlated with pulse rate (r = 0.2; p = 0.02) and waist:hip ratio (WHR; r = 0.2; p = 0.02). Taken together, smoking may worsen the already high risk for metabolic syndrome in women with PCOS.