Because of the advent of highly effective treatments, routine screening for HIV and hepatitis C virus (HCV) has been recommended for many Americans. This study explored the perceived barriers surrounding routine HIV and HCV screening in a diverse sample of community health centers (CHCs). The Community Health Applied Research Network (CHARN) is a collaboration of CHCs, with a shared clinical database. In July, 2013, 195 CHARN providers working in 12 CHCs completed a survey of their attitudes and beliefs about HIV and HCV testing. Summary statistics were generated to describe the prevalence of HIV and HCV and associated demographics by CHCs. HIV and HCV prevalence ranged from 0.1% to 5.7% for HIV and from 0.1% to 3.7% for HCV in the different CHCs. About 15% of the providers cared for at least 50 individuals with HIV and the same was true for HCV. Two-thirds saw less than 10 patients with HIV and less than half saw less than 10 patients with HCV. Less than two-thirds followed USPHS guidelines to screen all patients for HIV between the ages of 13 and 64, and only 44.4% followed the guidance to screen all baby boomers for HCV. Providers with less HIV experience tended to be more concerned about routine screening practices. More experienced providers were more likely to perceive lack of time being an impediment to routine screening. Many US CHC providers do not routinely screen their patients for HIV and HCV. Although additional education about the rationale for routine screening may be indicated, incentives to compensate providers for the additional time they anticipate spending in counseling may also facilitate increased screening rates.