Conventional HIV testing algorithms may be delayed or compromised in identifying HIV acquisition in the context of antiretroviral agent-based pre-exposure prophylaxis (PrEP). Data are available in delays of progression through the Feibig stages with the use of TDF/FTC PrEP, as well as lower viral load set points. Case reports of complete suppression of nucleic acid detection with PrEP use further complicate and delay diagnosis and set up complicated treatment decisions: True infection requires fully-suppressive cART regiments, yet in order to definitively make a diagnosis in the setting of discordant results, complete withdrawal of PrEP may be required. This latter decision is particularly fraught in high-risk populations where removal of prophylaxis may leave patients vulnerable to de novo HIV acquisition. Complexity will only increase in the future with long-acting PrEP agents. Novel testing methods will be required in the future.