Ug99 is a lineage of wheat stem rust (Puccinia graminis f. sp. tritici), which is present in wheat fields in several countries in Africa and the Middle East and is predicted to spread rapidly through these regions and possibly further afield, potentially causing a wheat production disaster that would affect food security worldwide. In 2005 the noted green revolution pioneer Norman Borlaug brought great attention to the problem, and most subsequent efforts can be traced to his advocacy. It can cause up to 100% crop losses and is virulent against many resistance genes which have previously protected wheat against stem rust.

Although Ug99-resistant varieties of wheat do exist, a screen of 200,000 wheat varieties used in 22 African and Asian countries found that only 5-10% of the area of wheat grown in these countries consisted of varieties with adequate resistance.

The original race of Ug99, which is designated as 'TTKSK' under the North American nomenclature system, was first detected in Uganda in 1998 and first characterised in 1999 (hence the name Ug99) and has since been detected in Kenya, Ethiopia, Eritrea, Sudan, Yemen, Iran, Tanzania, Mozambique, Zimbabwe, South Africa, and Egypt. There are now 15 known races of Ug99. They are all closely related and are believed to have evolved from a common ancestor, but differ in their virulence/avirulence profiles and the countries in which they have been detected.