Obesity is influenced by environmental, behavioral, and genetic factors; particularly genes related to the regulation of lipids and addictive behavior. Food craving (FC) is a physiological and behavioral response that triggers the intense desire to ingest food, particularly food with high energy, fat, and/or sweet content. Objective: To evaluate the relationship between the prevalence of FC in obese subjects and blood lipids as well as to determine the transcriptional modulation of CART, DRD2, and FTO. Method: Transverse, comparative, and randomized study including 21 obese participants (BMI, ≥30 kg/m2] and 20 normal weight participants (BMI, ≤25 kg/m2). We determined CART, DRD2, and FTO expressions; evaluated blood lipid levels; and obtained trait scores on the Food Craving Questionnaire-Trait, a multifactorial instrument validated for the Mexican population. Results: The DRD2 expression was significantly increased (p = 0.027) and the CART expression was significantly decreased (p = 0.001) in obese participants compared with normal weight participants. The FTO expression did not show significant differences. Food Craving Questionnaire-Trait showed scores of ≥72 in obese participants. Conclusions: Linear regression model analysis showed that FC is a predictor of atherogenic index (ATH), independently of BMI, and of the gene expression modulation of CART and DRD2.