A severe reduction in the populations of grey and ringed seals in the Baltic occurred during the 1960s and 1970s. Adult animals showed (and still show) a series of lesions inter alia in the female reproductive organs, intestines, integument, kidneys, adrenals, and skulls (the Baltic seal disease complex). The morphology and prevalence of light microscopic changes in the kidneys of 76 grey seals and 29 ringed seals collected in the Baltic proper and the Gulf of Bothnia during 1977–1996 are presented in this report. Specific changes in the glomeruli were diffuse thickening of the capillary walls and the presence of large, rounded, hyaline bodies in the capillary or capsular walls. Specific changes in the distal convoluted tubules and the collecting ducts included focal replacement of the normal epithelium by multilayered cell proliferations. The prevalence and extent of the changes were age-related and thus correlated with the time of exposure to environmental toxicants. The lesions were more conspicuous in Baltic grey seals than in Baltic ringed seals. Similar findings were recorded in 5 grey seals from Swedish zoological gardens. These animals had been fed Baltic fish for most of their lives. Electron microscopy was performed on 5 of the Baltic grey seals and on one of the grey seals from zoological gardens. Electron microscopy results mainly based on findings in one of the Baltic grey seals, included mesangial inter-position in the glomerular capillary walls and the characteristics of intercalated cells in cell proliferations in the distal parts of the nephrons. Eleven grey seals from the Scottish coast and 23 ringed seals from Svalbard served as reference material. None of the reference seals showed the specific lesions described above. The authors propose that organochlorine pollution of the Baltic environment is a factor in the cause of these kidney changes.