More than half of the 27,259 new infections, or 54 percent were recorded in France and Britain, with 5,750 and 8,925 cases respectively, said the EuroHIV centre.
The overall figure for the 27-nation European Union was 67.7 cases per million inhabitants, with the highest ratio in Estonia, 504.2 per million and 668 cases; and Portugal, 205 per million and 2,162 cases.
Slovakia and Hungary had the lowest rate with five per million, or 27 cases and eight per million, or 80 cases respectively.
France's rate of 91.9 per million inhabitants compared to Belgium's 95.3 per million (995 cases) and Switzerland's with 104.2 per million (757 cases).
With 66 percent men bore the brunt of the epidemic, and 11 percent of the new cases were diagnosed among 15- to 24-year-olds.
Heterosexual intercourse was the main source of infection with 42 percent, while infections due to sex between men accounted for 29 percent. Seven percent of infections were caused by intravenous drug use.
The overall caseload of more than 27,000 new infections includes figures from Iceland, Norway and Switzerland which are not members of the European Union.
UNAIDS, the global standard-bearer in the fight against HIV/AIDS, estimates the total number of people with HIV/AIDS in 2006 at 740,000 in western and central Europe and at 1.5 million in eastern Europe and central Asia.