Measurement of telomeres by polymerase chain reaction (PCR) amplification has been problematic due to the formation of dimers by the primers designed to hybridize to the telomere repeats. Recently, a set of primers that overcome this problem has been created and used to develop an assay to measure human telomeres by real-time quantitative PCR. We modified this assay to measure mouse telomeres. Results showed that the primers do indeed amplify mammalian telomere repeats without forming dimers. Results obtained from the real-time quantitative PCR assay of mouse DNA were similar to terminal restriction fragment analysis by pulsed-field gel electrophoresis followed by Southern hybridization. The assay performed with mouse DNA in a similar manner as it performs with human DNA. Preliminary linkage mapping suggests a gene influencing telomere length on the X chromosome. This assay will aid in the study of telomere function and importance in diseases associated with aging and cancer formation.