The aim of this cross-sectional study was to determine the prevalence of tonsillectomy among secondary school children and to investigate whether tonsillectomy with or without adenoidectomy is a risk factor for childhood obesity. A total of 27 secondary schools with 12,296 students between the ages 11 and 17 were screened in Denizli, Turkey. We determined 129 students who had undergone tonsillectomy; each student was matched with two healthy control subjects of the same age and sex (n = 258). A 28-item questionnaire on nutrition and physical exercise was completed by the parents. Age-adjusted body mass index and waist circumference percentiles of Turkish boys and girls were used for the assessment of overweight and obesity. The prevalence of tonsillectomy was 1.0 %. There was no significant relationship between having tonsillectomy and being overweight or obese and physical exercise and screen time (p > 0.05 for each). Logistic regression analyses suggested no significant effect of tonsillectomy on overweight or obesity of the subjects (p > 0.05). It seems that tonsillectomy had no effect on overweight and obesity among children.