Spironucleus muris is a flagellated protozoan belonging to the family Hexamitidae which commonly infects laboratory rodents. S.muris is found primarily in the crypts of the duodenum and pyloric glands and infection does not usually show any clinical signs. However, immunedeficient or weanling mice may exhibit diarrhoea, dehydration, weightloss, rough coat, lethargy, abdominal distention, hunched posture and sometimes death. S.muris has a direct development and transmission occurs through contact with infective cysts, most commonly through the faecal-oral route through ingestion of infective cysts. As little as one cyst is enough to cause infection. Prevalence of S.muris in laboratory and wild mouse populations ranges from 4 to 39% and large numbers of S. muris are often an indicator to an underlying disease or infection such as an MHV infection. Additionally, presence of the pinworm may indicate poor biosecurity management. As a result, fast and accurate diagnosis using real-time PCR would greatly aid those keeping and working with laboratory rodents.