Nuclear bud (NB) formation was investigated in blood erythrocytes of 1892 flounder Platichthys flesus, herring Clupea harengus, and eelpout Zoarces viviparus specimens that were collected at 82 sites representing different regions of the Baltic Sea in 2009-2011. This is the first attempt to evaluate the baseline levels of NB and rank the genotoxicity risk for native fish species. NB levels were compared to the previously published micronuclei (MN) data from the same individual fish specimens in order to compare the two methods of genotoxicity assessment and investigate the relationship between MN as the cytogenetic measure of genotoxicity and the DNA damage reflecting NB. In 2009-2011, elevated NB levels in 89.4% of flounder sampling groups indicated high and extremely high genotoxicity risk levels. Herring and eelpout sampling groups showed elevated levels of NB, 74.6 and 45.7%, respectively. In general, herring and eelpout NB measure was more sensitive as the genotoxicity biomarker than MN.