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Men who have sex with men (MSM), injection drug users (IDUs), and certain subgroups of heterosexuals are disproportionately affected by the syndemics of HIV, other sexually transmitted infections, and viral hepatitis. Although understanding the burden of these infections in these populations by urbanicity (the degree to which a geographic area is urban) is critical to targeting prevention programs, few studies have done so.We analyzed nationally representative 1999 to 2010 data from the National Health and Nutrition Examination Survey on persons aged 18 to 59 years. We estimated the weighted prevalence of HIV, herpes simplex virus type 2 (HSV-2), human papillomavirus, chlamydia, hepatitis B, and hepatitis C, stratified by urbanicity level, for the overall sample, MSM, IDUs, and heterosexuals. Geographic areas with population at least million are classified into large central and large fringe metropolitan counties.Overall, large central metropolitan areas had a higher prevalence of HIV, HSV-2, and hepatitis B. HIV prevalence among MSM was elevated in large central and large fringe metro areas (14.5% and 16.9%, respectively). Among heterosexuals, large central metropolitan areas had elevated prevalence of HSV-2, chlamydia, and hepatitis B. Human papillomavirus and hepatitis C prevalence did not vary significantly by urbanicity for any population, including IDUs.Infections with higher prevalence in urban areas merit a geographically focused approach to screening and prevention programs, whereas those with uniform prevalence across levels of urbanicity would benefit from a generalized prevention approach. These nationally representative, population-based data allow for more effective planning for prevention programs.