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The obesity epidemic is a global concern nowadays since obesity is a major risk factor that can cause many serious diseases. A high risk of developing diseases in an obese person primarily occurs due to metabolic disorders. As a rule, dyslipidemia acts as an early sign of metabolic disorders in case of obesity. Our research goal was to compare informative value of body mass index (BMI) and lipid accumulation product (LAP) for assessing atherogenic risks in lipid profile. Two thousand and four hundred people aged 20–60 years took part in our study. We determined participants’ anthropometric and clinical indicators and estimated lipid levels in blood serum. As expected, LAP values had a strong correlation with BMI values. Spearman’s rank correlation coefficient for LAP and BMI values amounted to 0.73 (< 0.001) in men (n = 1168) and 0.77 (< 0.001) in women (n = 1232). However, when we estimated agreement between these two indicators using Cohen’s Kappa coefficient, we established that this agreement between LAP and BMI values was rather low (0.35 for men and 0.39 for women). Having compared samplings with quartiles that differed as per LAP and BMI values, we detected that lipid profiles tended to be more atherogenic in people with LAP values being higher than BMI values. Given this established discordance in the quartiles, higher LAP values are associated with atherogenicity of lipid profile to a greater extent than values of BMI, the conventional obesity indicator. Using solely BMI to diagnose obesity may result in underestimating metabolic disorders in the body. To assess obesity and metabolic health correctly, it is advisable to determine LAP value together with traditional obesity indexes.