The objective was to investigate the genetic relationships among Echovirus 6 (E6) strains circulating in Greece and to compare them with the respective strains from other geographic regions. Cerebrospinal fluid samples collected during the period 2006-2007 from 84 patients with aseptic meningitis or encephalitis were tested for a probable enteroviral infection. Two RT-PCRs amplifying overlapping regions of the VP1 gene were performed, while isolation procedures were applied in one third of cases. All PCR products were sequenced, and further phylogenetic analysis was performed for E6 strains. Enteroviruses were detected in 27 out of 84 cases (32.14%) and E6 was the predominant serotype (11 out of 27, 40.74%). Three distinct clades of Greek E6 sequences were seen in the phylogenetic tree: sequences of the present study were placed in clades A and B, while sequences of a former study in Greece were clustered in clade C. Sequences of clades A and C presented high genetic homology (>95%) with sequences from other countries, while sequences of clade B were unique, differing by more than 15% from all known E6 sequences. The most prevalent enterovirus in Greece during the period 2006-2007 was E6, and was associated with aseptic meningitis. A high degree of heterogeneity was observed among Greek E6 strains.