Background To evaluate the association between diet and disease, the consideration of a whole diet has appeared to be more effective than the examination of single-nutrient intake. This study aimed to examine the relationship between dietary diversity score (DDS) and obesity in Iranian children. Methods A cross-sectional study was conducted on 456 children aged 11–18 years, who were selected by random cluster sampling. The usual food intake for each participant assessed using a validated Food frequency questionnaire (FFQ). To calculate the dietary diversity score, food items were categorized into 5 broad groups and 23 subgroups based on the US Department of Agriculture Food Guide Pyramid. Participants were categorized based on the DDS tertile cut-off points. Anthropometric measurements were conducted based on standard protocols. Overweight and obesity were defined as 85th ≤ BMI < 95th, and ≥ 95th percentiles of BMI, respectively. Additionally, abdominal obesity was considered as WC ≥ 85th percentile. Results Mean and standard deviation (SD) of subjects’ Body Mass Index (BMI) and waist circumference were 20.88 (SD 4.22) kg/m2 and 74.27 (SD 10.31) cm, respectively. The probability of overweight and obesity was increased as tertiles of DDS increased (OR among tertiles: 1.00, 1.82 and 2.13 for overweight and 1.00, 2.60 and 3.45 for obesity; this was the same for abdominal obesity: 1.00, 2.22 and 3.45, P <  0.001 for all). However, no statistically significant results were found after adjustment for energy intake. Conclusion Dietary diversity positively affected obesity through higher energy intake. Despite the wide recommendation of having high dietary diversity, public health programs should emphasize to improve dietary diversity only in selective food items.

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