While in office, Mbeki and his former Health Minister Manto Tshabalala-Msimang, nicknamed "Dr. Beetroot," were accused of denying that the HIV virus causes acquired immune deficiency syndrome (AIDS), despite conclusive scientific evidence on the matter. 
Akiwa madarakani, Mbeki na waziri wake wa zamani wa Afya Manto Tshabalala-Msimang, aliyepachikwa jina la utani "Dk. Magimbi," walituhumiwa kwa kupinga kwamba Virusi Vya UKIMWI (VVU) vinasababisha UKIMWI, pamoja na kuwepo ushahidi wa kisayansi unaothibitisha suala hilo.