Since 2004/2005 a worldwide shift of the detection rate of porcine circovirus (PCV) has been observed from PCV2a towards PCV2b. Currently commercially available vaccines are based on genotype PCV2a. The study was conducted as a pilot study to evaluate the occurrence of PCV2a and PCV2b in farms with different vaccination strategies against PCV2.For this purpose a total of 405 piglets originating from nine farms (three farms with sow vaccination [SI], piglet vaccination [FI] and no vaccination [NI] against PCV2, respectively) were enrolled and followed from day 3 of life until slaughter. Serum of the piglets was examined for PCV2-DNA by quantitative PCR, genotype differentiating duplex PCR, and after sequencing of the total genome, PCV2 isolates were phylogenetically assigned. The evaluation included the data from 383 animals.In eight farms PCV2 could be detected (1x PCV2a; 6x PCV2b; 1x PCV2a and PCV2b). PCV2b was found in SI-, NI- and FI-farms, whereas PCV2a was only detected in SI- and NI-farms. A proportion of 55.4% was PCV2-positive at least once during the entire study period (FI: 7.8%, SI: 65.4%, NI: 93.7%). Of these samples 4.7% were PCV2a-, 92.2% PCV2b- and 2.4% PCV2a- and PCV2b-positive. The mean content of PCV2-DNA in the serum of PCV2b positive animals was significantly higher than from PCV2a positive animals. PCV2 isolates were identified as PCV2b-1A (5/9 farms), PCV2b-1B (1/9 farms) und PCV2a-2D (2/9 farms).The increased detection rate of PCV2b in comparison to PCV2a could be confirmed. The present study gives hint that the vaccination of piglets using PCV2a-based vaccines may lead to a further shift of the detection rate from PCV2a to PCV2b. To assess the clinical relevance of this observation, extensive comparative studies should be taken into account, which also evaluate the efficacy of PCV2a-based vaccines in PCV2a- and PCV2b-positive farms.