South Africa has the third highest tuberculosis (TB) and the fifth highest drug-resistant tuberculosis (DR-TB) burden in the world. The increase of DR-TB is largely due to the HIV epidemic and the challenges that are faced with the management of the disease. KwaZulu-Natal (KZN) and the Eastern Cape (EC) have the highest burden of DR-TB cases in South Africa. During 2005-2008 the “Preserving the Effective TB Treatment Study” (PETTS) was conducted in order to determine the rate of, risk factors for and consequences of acquired resistance to second-line drugs in MDR-TB patients in the EC and KZN. The study results are presented here.