This article aims to introduce and demonstrate the application of the standardization and decomposition analysis (SDA) method to gauge differences in HIV prevalence rates among injection drug users (IDUs) across regions (Northeast, South, Midwest, and West) in the U.S. Using the SDA, the regional HIV prevalence rates were standardized and a rate difference between regions was decomposed into component effects, such as the “real” rate difference, and component effects attributed to differences in specific compositions of confounding factors. A total of 9,824 injection drug users (IDUs) retrieved from the national database of the National Institute on Drug Abuse’s Cooperative Agreement for AIDS Community-Based Outreach/Intervention Research Program (COOP) projects constitute the sample for the study. A computer program DECOMP was used to implement the multi-population SDA.