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Tandem repeats (TRs) are a significant source of genetic variation in the human population, and TR alleles are responsible for over 60 human genetic diseases and for inter-individual differences in many biomedical traits. Therefore, we utilized long-read sequencing and state of the art computational programs to produce a database with 2,528,854 TRs covering 39 inbred mouse strains. As in humans, murine TRs are abundant and were primarily located in intergenic regions. However, there were important species differences: murine TRs did not have the extensive number of repeat expansions such as those associated with human repeat expansion diseases, and they were not associated with transposable elements. We demonstrate by analysis of two biomedical phenotypes, which were identified over 40 years ago, that this TR database enhances our ability to characterize the genetic basis for trait differences among inbred strains.