The body mass index (BMI) is an imperfect clinical measure of obesity that should be used in conjunction with other valid measures of weight-related risk. We studied whether there is a superior measure of obesity-related comorbidities. Records of bariatric clinic patients who had an abdominal computed tomography (CT) within 1 year of visit were reviewed. The presence of obesity-related comorbidities was determined at the time of the scan. BMI and ponderal index (PI) were calculated, and CT scans were reviewed to determine the visceral cross-sectional area (VCSA), subcutaneous fat cross-sectional area (SFCSA), and liver volume (LV). Data were analyzed using the Kruskal-Wallis test and Mann-Whitney U test. A higher number of comorbidities were found to be associated with a larger BMI (P = .011), VCSA (P = .014), SFCSA (P = .007), and LV (P = .014), but not a larger PI (P = .11). Of the 16 comorbidities assessed, VCSA and LV were associated with more than BMI and SFCSA. However, each measure could be associated with different comorbidities. A higher BMI was associated with increased insulin use (P = .034), hypertension (P = .007), and history of obstructive sleep apnea (P = .015), none of which were associated with PI. BMI and PI were the only measures associated with a history of deep vein thrombosis/pulmonary embolism (both P < .01). Only SFCSA was found to be associated with gastroesophageal reflux disease (P = .029). VCSA (P = .038) and LV (P = .001) were associated with nonalcoholic fatty liver disease. No measure could account for all obesity-related comorbidities, implying the need for targeted measurements. However, PI was the least effective measure.