Studies of birds from Doñana (southwestern Spain) after the Aznalcóllar mining accident (April 1998) have reported high levels of genetic damage when compared to conspecifics from reference areas. However, potential relationships between DNA damage and metal pollution have not yet been reported. The aim of the present study was to investigate the current levels of Zn, Pb, As, Cu, and Cd and to determine if they were associated with the genetic damage observed in free-living, nestling white storks (Ciconia ciconia) and black kites (Milvus migrans) born in the Doñana area after the mining spill. Blood concentrations of heavy metals and of As were quantified and DNA damage (comet assay) was determined in 258 storks and 132 kites monitored during a four-year period (1999-2002). Correlations between these elements and genetic damage varied between species and throughout years within species. Some elements did not show any relationship with DNA damage (e.g., Pb), whereas others had a significant correlation (e.g., As in storks, and Cu and Cd in kites) or only marginal statistical effects (e.g., Zn and Cd in storks, and As in kites) in some years but not in others. These results suggest that nestling white storks and black kites were affected, in part, by the elements studied, but they alone do not satisfactorily explain the observed DNA damage. Moreover, our results show that species-specific differences should be carefully considered when planning schemes for pollution monitoring, and highlight the need for including the temporal scale into the study of the pollutants effects in the wild.