The origin of the progressive spinocerebellar ataxic disorder 'Machado Joseph Disease (MJD)' has been attributed solely to an expansion mutation resulting from an autosomal dominant inheritance of an unstable CAG repeat in chromosome 14q32.1 of the MJD gene that encodes for the synthesis of ataxin 3. The faulty gene has purportedly been disseminated since the Middle Ages into Azorean, Dutch and Makassan communities by an international trading community based in NE-central Portugal. However, following improvements in MJD surveillance, the MJD afflicted families that have been identified in increasing numbers of familial clusters of MJD being discovered around the world--e.g. in Aboriginal, Yemenite, Asian and Japanese populations--cannot be connected back to the original Portuguese founder families, but rather implicates an environmental factor, superimposed on a genetic flaw. An analytical study of the isolated ecosystems supporting both the Portuguese and non-Portuguese MJD affected communities demonstrates a common abnormal hallmark of high manganese (Mn)/low magnesium (Mg) status, suggesting that this aberrant mineral ratio inactivates the Mn/Mg catalyzed endonuclease 1 enzyme in the biosystems of those who are dependent upon these ecosystems. Endonuclease activity is crucial for protecting against the expansion/contraction of the trinucleotide repeats in the genes that encode for proteins such as Ataxin 3--the 'mutant' chaperone protein that hallmarks the central nervous system (CNS) of MJD sufferers. It is proposed that MJD, and possibly the other more common expansion mutation diseases such as Friedrich's Ataxia and Huntingdon's Chorea, are multifactorial diseases caused by a hitherto unrecognised autosomal dominant inherited failure to regulate Mn/Mg metabolism in populations living in high Mn/low Mg ecosystems. Mg supplementation of the 'at risk' populations during the 'in utero' developmental stages could be all that is required to maintain healthy endonuclease turnover, thereby protecting MJD susceptible genotypes against this fatal, progressive neurodegenerative disease.