This study examined the association between intestinal lactobacilli and obesity dependent on dietary patterns in children. A cross-sectional study was conducted including 1111 children, 6-12 years old. Obesity was determined according to the WHO cut-off points. Diet information from a Food Frequency Questionnaire identified three dietary patterns. Lactobacillus sp. were determined by a real-time polymerase chain reaction (PCR). The consumption of complex carbohydrates and a high abundance of L. paracasei were associated with a lower risk of obesity (0.35, Confidence Interval 95% 0.19-0.65). The same happened with a medium consumption of fats and a medium abundance of L. paracasei (0.43, CI95% 0.24-0.78). In contrast, an increased risk of obesity is observed with a medium and high consumption of simple carbohydrates (2.37, CI95% 1.29-4.34 and 2.52, CI95% 1.36-4.66, respectively, p-trend