The vast majority of individuals infected with human T-cell lymphotropic virus type 1 have a strong and persistently activated cytotoxic T lymphocyte response to the virus. Experimental work investigating the effects of human T-cell lymphotropic virus-specific cytotoxic T lymphocytes is conflicting. One significant body of work suggests that specific cytotoxic T lymphocytes are protective and help to reduce the risk of disease. However, another body of work implies that specific cytotoxic T lymphocytes play an important role in the development of disease. Here we use a theoretical model to explore the role of cytotoxic T lymphocytes in persistent infection. A way of reconciling the apparently contradictory data is proposed and experimentally testable predictions are made.