Due to the increase in obesity worldwide, international organizations have promoted the adoption of a healthy lifestyle, as part of which fruit consumption stands out. However, there are controversies regarding the role of fruit consumption in mitigating this disease. The objective of the present study was to analyze the association between fruit intake and body mass index (BMI) and waist circumference (WC) in a representative sample of Peruvians. This is an analytical cross-sectional study. Secondary data analysis was conducted using information from the Demographic and Health Survey of Peru (2019–2021). The outcome variables were BMI and WC. The exploratory variable was fruit intake, which was expressed in three different presentations: portion, salad, and juice. A generalized linear model of the Gaussian family and identity link function were performed to obtain the crude and adjusted beta coefficients. A total of 98,741 subjects were included in the study. Females comprised 54.4% of the sample. In the multivariate analysis, for each serving of fruit intake, the BMI decreased by 0.15 kg/m2 (β = −0.15; 95% CI −0.24 to −0.07), while the WC was reduced by 0.40 cm (β = −0.40; 95% CI −0.52 to −0.27). A negative association between fruit salad intake and WC was found (β = −0.28; 95% CI −0.56 to −0.01). No statistically significant association between fruit salad intake and BMI was found. In the case of fruit juice, for each glass of juice consumed, the BMI increased by 0.27 kg/m2 (β = 0.27; 95% CI 0.14 to 0.40), while the WC increased by 0.40 cm (β = 0.40; 95% CI 0.20 to 0.60). Fruit intake per serving is negatively related to general body adiposity and central fat distribution, while fruit salad intake is negatively related to central distribution adiposity. However, the consumption of fruit in the form of juices is positively associated with a significant increase in BMI and WC.
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