Background: The aim of this study was to evaluate the presence of variable strains of GBV-C among blood donors in Lower Saxony (Northern Germany) and to study the genetic variability. Material and Methods: Sera of 1,011 volunteer blood donors were tested for GBV-C genomes by RT-PCR using primer pairs which amplify portions of the NS5a and 5''-NCR regions. Results: A frequency of 1.98% GBV-C-positive blood donors was observed. While the Lower Saxony strains were relatively conserved in the 5''-NCR region, the NS5a region showed a higher degree of diversity. Conclusions: Phylogenetic sequence analysis revealed that Lower Saxonian, Spanish and North American GBV-C strains were relatively closely related and showed a great diversity to Asian GBV-C isolates.