Obesity impacts on many issues of pulmonary medicine, where it is debated if obesity is linked to asthma, atopy or altered lung function tests. Our study aimed to investigate primarily the effect of obesity on the lung function tests and secondary the possible link of obesity with atopy and asthma in a large cohort of children in Greece. Body mass index (BMI) and data from a questionnaire for lung health, atopy, nutritional habits and family history were obtained from 2,715 children aged 6-11 years. Six hundred fifty-seven children with BMI>85th percentile (357 overweight, 300 obese) and a group of 196 normal weight children underwent spirometry. The % expected FVC, FEV(1), FEF(25-75), and FEV1/FVC were significantly reduced in overweight or obese children compared to children with normal weight (P = 0.007, P < 0.001, P < 0.001, and P < 0.001, respectively). Reported atopy was significantly higher in overweight or obese children compared to normal weight children (P = 0.008). High BMI remained a strong independent risk factor for asthma (OR = 2.17, 95% CI = 1.22-3.87, P = 0.009) and for atopy (OR = 2.06, 95% CI = 1.32-3.22, P = 0.002). The effect of increased BMI on asthma was significant in girls, but not in boys (OR = 2.73, 95% CI = 1.09-6.85, P = 0.032; OR = 1.74, 95% CI = 0.83-3.73, P = 0.137, respectively). In conclusion we have shown that high BMI remains an important determinant of reduced spirometric parameters, a risk factor for atopy in both genders and for asthma in girls.