This atlas represents a first step in comparing the anatomic organization of the brains of the C57BL/6 and the 129/Sv mice, two substrains that are frequently used in studies of the central nervous system. The mouse is rapidly becoming the most commonly used mammalian resource in biomedicine. The need to model human diseases through genetic manipulation in transgenic animals, the existence of a wide array of immunological markers for murine cell surface receptors, and the need to test new drugs has resulted in an increasing demand for inbred rodents. To date, a very large number of genetically manipulated mouse models have been created, that have been derived from over 450 inbred strains. Whereas it is possible to control the expression of specific genes in these animals, relatively scarce information is known on the comparative neuroanatomical characteristics of different strains of mice.Such information is crucial for the interpretation of scientific data obtained from genetically manipulated animals. Because many such genetically manipulated mice models are used in neuroscience, it is important to document the differences in brain organization existing among different mouse strains.Representative series of 49 levels for general cytoarchitecture and 6 levels for myeloarchitecture are presented in standard stereotaxic coordinates from the brains of the C57BL/6 and the 129/Sv mice. This permits a comparison of the distribution of the various nuclei, cortical areas and fiber tracts, and an assessment of the variability between the two strains. For each plate, an alphabetical list of structures, with the abbreviations used in the plate and the full anatomical names of the structures is provided. An alphabetical index of structure names for each mouse with relevant atlas pages is included as well as a comparative list of structures in alphabetical order with indication of the pages and levels calculated from the bregma where structures occur. This permits a quick cross-reference of the extent and location of specific brain structures between the two mice.Matching CD-ROMs, containing all of the plates in Adobe Illustrator 8.0 format, structure lists and comparative index are also provided.In future this atlas will be enriched with brains of other mouse strains and eventually provide comparative and quantitative, stereologic as well as immunohistochemical data on a series of relevant brain structures.