The Centers for Disease Control and Prevention recently released the first direct national estimate of HIV incidence. Local jurisdictions have begun to apply this methodology. The national and local estimates have been higher than assumed. When applied to San Francisco, there were 935 new HIV infections [95% confidence interval (CI) 658-1212] during 2006. We compared this incidence estimate to an estimate produced in San Francisco in 2006 by a panel of HIV researchers using an iterative Delphi method. Results were similar. Further corroboration of the new method in local areas would strengthen interpretation and identify HIV risk variations.