Abstract In horses, muscle biopsy is widely used in veterinary practice for routine diagnosis of various muscle disorders. Development of genetic methods such as gene expression measurements using microarrays, RNA-seq, and real-time PCR leads to searching an alternative, less invasive biopsy method in order to obtain an appropriately representative group of animals for genetic testing. In the present study, we proposed a minimally invasive method of muscle sample biopsy using Pro- MagTM Ultra Automatic Biopsy Instrument (Surgical Specialties Corporation, US, Inc.), which is commonly utilized in human medicine. This approach does not require skin incisions and usage of stitches. The quantity of muscle sample gained in accordance with presented procedure was sufficient to obtain RNA with a good quality. Furthermore, application of the automatic biopsy instrument allows obtaining a sufficient amount of biological material for genetic analysis from a wide variety of tissues. Moreover, samples acquired according to this method could be used in other analyses.