The maintenance and preservation of strains of mice used in biomedical research presents a unique challenge to individual investigators and research institutions. The goal of this study was to assess a comprehensive system for mouse strain conservation through a combination of natural mating, sperm cryopreservation and assisted reproductive technology. Our strategy was based on the collection and cryopreservation of fresh epididymal sperm from male mice by semi-vasectomy; these mice were then naturally mated for breeding purposes. If no satisfactory results were obtained from natural breeding, then the cryopreserved sperm were used for in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI); resultant embryos were then transferred into pseudopregnant-recipient female mice. Our results show that some semi-vasectomized mouse strains can be conserved by natural breeding, and that sterile males can be compensated for through the use of IVF and ICSI technology. As such, we believe this system is suitable for the purpose of strain conservation, allowing the continuation of natural breeding with the safeguard of assisted reproduction available.