The prevalence of carriers of three genetic disorders, severe combined immunodeficiency, lavender foal syndrome and cerebellar abiotrophy, in registered, purebred Arabians in South Africa was assessed. Genotyping for the three disorders was performed on individuals randomly selected from two populations: purebred Arabian horses born in South Africa during the intervals 1 August 2004 to 31 July 2005 and 1 August 2009 to 31 July 2010, in line with physiological breeding seasons. This permitted an estimation of the change in prevalence of each disorder between 2004 and 2009, during which time compulsory testing for SCID, and selective breeding based on the results thereof, was performed. The prevalence of lavender foal syndrome and cerebellar abiotrophy for the 2009 breeding season was found to be 11.7% (95% confidence interval [CI] 7.80 – 16.37) and 5.1% (95% CI 2.56 – 8.69) respectively, with no statistically significant change in the prevalence of these disorders between 2004 and 2009. Utilizing a larger sample size, the prevalence of severe combined immunodeficiency was found to have decreased significantly from 6.4% (95% CI 6.05 – 6.78) in 2004 to 3.4% (95% CI 2.67 – 4.23) in 2009 (P < 0.0001). These results will encourage the genetic screening of Arabian horses intended for breeding purposes in order to prevent the birth of clinically affected individuals. This study also highlights the usefulness of genetic testing as a tool to decrease the prevalence of specific genetic disorders within animal populations.