The blood cell phosphatidylinositol glycan class A (PIG-A) gene mutation assay has been extensively researched in rodents for in vivo mutagenicity testing and is now being investigated in humans. The PIG-A gene is involved in glycosyl phosphatidylinositol (GPI)-anchor biosynthesis. A single mutation in this X-linked gene leads to loss of membrane bound GPI-anchors, which can be enumerated using flow cytometry. With many studies published to date measuring this mutation in erythrocytes, there is remarkable consistency across research groups. Moreover, with the low background level of mutant erythrocytes in healthy subjects (2.9 - 5.56 x 10-6 mutants), induction of mutation post genotoxic exposure can be detected. Cigarette smoking, radiotherapy and occupational exposures including lead, have been shown to increase mutant levels. Identification of harmful agents can allow us to recommend new exposure limits, minimising individual risk. Conversely, protective agents such as aspirin and healthy diets could mitigate these effects, reducing baseline somatic mutation levels and such behaviours can be encouraged. This mutational monitoring approach may also provide information on individuals at higher risk of cancer development. Patients with inflammatory bowel disease, oesophageal adenocarcinoma and pancreatic cancer have elevated numbers of PIG-A mutant erythrocytes compared to age-matched controls. With further technological progress including protocol standardisation and the development of cryopreservation methods to improve GPI-anchor stability, this assay can be widely employed in rural and low-income countries. Here we review the current literature on PIG-A mutation in human subjects and discuss the potential role of this assay in human biomonitoring and disease.