Doñana Park (Spain), a protected area in Europe, was affected by an environmental disaster in April 1998 that caused the spreading of acidic water and mud full of toxic metals from the Aznalcollar pyrite mine. In order to assess the contamination in the area and to monitor the possible biological effects of the toxic spill, a series of coordinated studies was performed utilizing several animal species living in that area. We performed genotoxicity monitoring using the Comet assay on peripheral blood leukocytes of the Algerian mouse (Mus spretus), a nonprotected rodent suitable as a bioindicator. The mice were sampled in different areas 6 months after the ecological disaster and again 1 year later. Our results showed that in 1998 all the areas examined were contaminated, as determined by an increase in the Comet assay parameters in the analyzed animals, whereas a significant decrease in the values of these parameters was observed in the 1999 samples, which were collected in a riverside area subject to tide flows. Thus, the Comet assay has proven to be an interesting and sensitive tool in studies of environmental genotoxicity.