National rates from human immunodeficiency virus (HIV) and sexually transmitted disease (STD) surveillance may not effectively convey the impact of HIV and STDs on American Indian/Alaska Native (AI/AN) communities. Instead, we compared average annual diagnosis rates per 100,000 population of HIV, chlamydia (CT), gonorrhea (GC), and primary and secondary (P&S) syphilis, from 2007 to 2010, among AI/AN aged ≥ 13 years residing in 625 counties in the 12 Indian Health Service Areas, all AI/AN, and all races/ethnicities to address this gap. AI/AN comprised persons reported as AI/AN only, with or without Hispanic ethnicity. Out of 12 IHS Areas, 10 had higher case rates for CT, 3 for GC, and 4 for P&S syphilis compared to rates for all races/ethnicities. Eight Areas had higher HIV diagnosis rates than for all AI/AN, but HIV rates for all IHS Areas were lower than national rates for all races/ethnicities. Two IHS Areas ranking highest in rates of CT and GC and four Areas with highest P&S syphilis also had high HIV rates. STD and HIV rates among AI/AN were greater in certain IHS Areas than expected from observing national rates for AI/AN. Integrated surveillance of overlapping trends in STDs and HIV may be useful in guiding prevention efforts for AI/AN populations.