PCV-2 is considered one of the most economically important viral agents in swine worldwide. Recently, PCV-3 has been found in pigs affected by different disorders and in healthy animals. The objective of this epidemiological work was to describe the frequency of detection of PCV-2 and PCV-3 in pig farms of 9 European countries. Moreover, a second aim was to assess the most frequent PCV-2 genotypes found in the studied farms. Sera from 5 to 10 pigs per farm were collected from 2 to 11 farms per studied country. A total of 624 sera of fattening pigs (10-25 week old) from 64 farms from Spain (n = 11), Belgium (n = 10), France (n = 8), Germany (n = 8), Italy (n = 7), Denmark (n = 8), the Netherlands (n = 5), Ireland (n = 5) and Sweden (n = 2) were analysed by conventional PCR. In addition, one or two PCV-2-positive samples per farm were genotyped by sequencing the ORF2 gene. PCV-3 PCR-positive samples with relatively low Ct values were also sequenced and phylogenetically analysed. PCV-2 DNA was detected in pig sera from all European tested countries, but Sweden. A total of 132 out of 624 (21%) sera were positive for PCV-2 PCR, corresponding to 30 out of the 64 (47%) tested farms. PCV-3 DNA was detected in 52 out of 624 (8%) sera, corresponding also to 30 out of the 64 (47%) studied farms from all tested countries. A total of 48 PCV-2 PCR-positive samples were successfully sequenced and genotyped, being PCV-2d the most frequently genotype found (n = 28), followed by PCV-2b (n = 11) and PCV-2a (n = 9). These results pointed out PCV-2d as the most prevalent genotype currently in Europe. The PCV-3 phylogenetic analysis showed high identity (>98%) among sequences from all the analysed countries. The relatively low co-infection (3%), likely suggest an independent circulation patterns of PCV-2 and PCV-3.