Objectives. We assessed neighborhood confounding on racial/ethnic obesity disparities among adults in New York City after accounting for complex sampling, and how much neighborhood factors (walkability, percentage Black or Hispanic, poverty) contributed to this effect. Methods. We combined New York City Community Health Survey 2002-2004 data with Census 2000 zip code-level data. We estimated odds ratios (ORs) for obesity with 2 sets of regression analyses. First, we used the method incorporating the conditional pseudolikelihood into complex sample adjustment. Second, we compared ORs for race/ethnicity from a conventional multilevel model for each neighborhood factor with those from a hybrid fixed-effect model. Results. The weighted estimate for obesity for Blacks versus Whites (OR = 1.8; 95% confidence interval = 1.6, 2.0) was attenuated when we controlled neighborhood confounding (OR = 1.4; 95% confidence interval = 1.2, 1.6; first analysis). Percentage of Blacks in the neighborhood made a large contribution whereas the walkability contribution was minimal (second analysis). Conclusions. Percentage of Blacks in New York City neighborhoods explained a large portion of the disparity in obesity between Blacks and Whites. The study highlights the importance of estimating valid neighborhood effects for public health surveillance and intervention.