Objectives: Transmitted HIV drug resistance may impair treatment efficacy of combination antiretroviral therapy (ART). This study describes the epidemiology of transmitted resistance in chronically infected patients. Methods: In a prospective multicenter trial in Nordrhein-Westfalen, Germany, transmitted drug resistance was determined by genotypic resistance testing in patients on initiation of first-line ART. Results: From 2001 to 2009, 2,078 patients were enrolled in the study. 79.9% were male, 81.2% were Caucasians, and a homosexual transmission mode was found in 51.3%. Of these patients, 41.5% were at the stage of AIDS, median CD4 cell count was 230/µl, and median viral load was 64.466 copies/ml. Transmitted drug resistance mutations were seen in 9.2% (95% CI, 7.9–10.4). Resistance in the nucleoside reverse transcriptase inhibitor class was found in 5.8% (4.8–6.8), in the nonnucleoside reverse transcriptase inhibitor class in 2.8% (2.1–3.6), and in the protease inhibitor class in 2.7% (2.0–3.4). After a continuous increase to a level above 10% in the years 2006 and 2007, a decline of drug resistance prevalence followed in 2008 and 2009. Conclusions: Transmitted HIV drug resistance was found in around 10% of chronically infected patients in Germany who started their ART. We showed a moderate decline of the prevalence of mutant virus strains in recent years. Further surveillance of this phenomenon is mandatory.