If i have cystic fibrosis and get a lung transplant, will the disease eventually invade my new lungs?

No: The risk to the transplanted lungs are infection from bacteria left over from the old lungs, and acute and chronic rejection of the new lung by the body. Cystic fibrosis is a defect that is limited to the old lungs.

It can: Lung transplant for CF is an important life prolonging therapy but it exchanges one set of problems for another. After transplant, there is risk of rejection of the transplanted lungs by one's own immune system requiring use of strong meds that suppress your immune system which then increases your risk of serious infections. There are many facets to this - talk to your CF dr to discuss pros/cons.

Trachea still CF: The graft of new lungs does leave a trachea that still has the CF defect. This can serve as a source of infection to the new lungs. The new transplanted lungs though will not have CF disease.