Minisatellites are tandemly repeated DNA sequences that are found in most higher eukaryotes. They are genetically unstable and often gain or lose repeat units. Minisatellite repeats contain a "core" sequence which is highly conserved among a family of minisatellites. The core sequence resembles the chi sequence of Escherichia coli which is a binding site for recombination proteins. It has therefore been suggested that minisatellite core sequences may also be binding sites for proteins involved in recombination. In this paper, we report several proteins in mouse brain, liver, and kidney nuclear extracts which bind to various minisatellite sequences. We have found several proteins which have not been previously reported and, in addition, have noted that brain has a different profile of minisatellite-binding proteins than liver and kidney. Moreover, we have also observed probe-specificity in the binding of some of these proteins, suggesting that different "families" of minisatellites may have qualitatively different functions.