OK, this often causes confusion, so I'll try to explain.
In the medical sense, endogenous can be said to mean something that grows within the body. However, it also refers to something arising from within the body or produced from internal causes, such as a disease caused by the failure of an organ or system.
An endogenous infection is an infection caused by the reactivation of previously dormant organisms within the body. An example is tuberculosis as most cases of clinical TB nowadays are considered to be the result of dormant, endogenous infections. Other examples are Leishmaniasis and Shingles