Federally qualified health centers play an important role in providing health care to underserved populations. Recent substantial federal investments in health information technology have enabled health centers to expand their use of electronic health record (EHR) systems, but factors associated with adoption are not clear. We examined 2010–12 administrative data from the Health Resources and Services Administration’s Uniform Data System for more than 1,100 health centers. We found that in 2012 nine out of ten health centers had adopted a EHR system, and half had adopted EHRs with basic capabilities. Seven in ten health centers reported that their providers were receiving meaningful-use incentive payments from the Centers for Medicare and Medicaid Services (CMS). Only one-third of health centers had EHR systems that could meet CMS’s stage 1 meaningful-use core requirements. Health centers that met the stage 1 requirements had more than twice the odds of receiving quality recognition, compared with centers with less than basic EHRs. Policy initiatives should focus assistance on EHR capabilities with slower uptake; connect providers with technical assistance to support implementation; and leverage the connection between meaningful use and quality recognition programs.