Infection of pigs with porcine circovirus type 2 (PCV2) causes a variety of disorders collectively referred to as porcine circovirus associated diseases (PCVADs). PCV2 isolates can be classified into two major types: PCV2a and PCV2b. In the present study, effects of vaccination on antibody titers in sera, PCV2 viremia, and shedding of PCV2 in feces were studied on Japanese commercial pig farms where vaccination of piglets against PCV2 was performed using commercially available vaccines. The effectiveness of vaccination against various PCV2 genotypes was also assessed. Among the 16 farms studied, 10 and 6 had been infected with PCV2a and PCV2b, respectively. PCV2a was further subdivided into PCV2a-1 and PCV2a-2. PCV2a-1 and PCV2a-2 prevailed on 6 and 4 farms, respectively, among the 10 farms infected with PCV2a. The PCV2 vaccines were effective in reducing PCV2 infection on commercial pig farms. Mean mortality rates were significantly decreased over 8 months after the start of the PCV2 vaccination program as compared to those before the start of the PCV2 vaccination program on farms infected with PCV2a-2 (20.8% vs. 12.1%) and PCV2b (26.5% vs. 13.7%). On the farms with PCV2a-1 infected pigs, there was no significant difference in the mean mortality rate before versus after the start of the vaccination program (14.7% vs. 14.1%). Mortality rate reduction with the PCV2 vaccination might depend on the genetic types of PCV2.