Objective To investigate the hepatitis B virus (HBV) infection data of part of secondary hospital and above in Beijing for clinical treatment and prevention. Methods 3351 patients’ samples from Jan. 2011 to Dec. 2013 were selected to take real-time fluorescent quantitative PCR amplification for HBV-DNA measurement. The result of 5×102 IU/mL was setup as a positive standard. Results The HBV infection rate of secondary hospital and above was about 33.42% in Beijing from year 2011 to 2013. The infected numbers of men were higher than that of women. Patients mainly come from the age 21 to 40. The infected numbers were reduced after the Immunization Plan. Conclusion The HBV infection rate in Beijing is high. It is suggested to control the viral replication of HBV positive population and also protect susceptible population from infection.