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Nationally representative data on the quality of care for obese patients in US-ambulatory care settings are limited. We conducted a cross-sectional analysis of the 2005 and 2006 National Ambulatory Medical Care Survey (NAMCS). We examined obesity screening, diagnosis, and counseling during adult visits and associations with patient and provider characteristics. We also assessed performance on 15 previously published ambulatory quality indicators for obese vs. normal/overweight patients. Nearly 50% (95% confidence interval (CI): 46–54%) of visits lacked complete height and weight data needed to screen for obesity using BMI. Of visits by patients with clinical obesity (BMI ≥30.0 kg/m2), 70% (66–74%) were not diagnosed and 63% (59–68%) received no counseling for diet, exercise, or weight reduction. The percentage of visits not being screened (48%), diagnosed (66%), or counseled (54%) for obesity was also notably higher than expected even for patients with known obesity comorbidities. Performance (defined as the percentage of applicable visits receiving appropriate care) on the quality indicators was suboptimal overall. In particular, performance was no better than 50% for eight quality indicators, which are all related to the prevention and treatment of obesity comorbidities, e.g., coronary artery disease, hypertension, hyperlipidemia, asthma, and depression. Performance did not differ by weight status for any of the 15 quality indicators; however, poorer performance was consistently associated with lack of height and weight measurements. In conclusion, many opportunities are missed for obesity screening and diagnosis, as well as for the prevention and treatment of obesity comorbidities, in office-based practices across the United States, regardless of patient and provider characteristics.