Toxoplasmosis is a rare but life-threatening complication of allogeneic stem-cell transplantation. Polymerase chain reaction (PCR) offers the possibility to make the diagnosis earlier than conventional techniques, and is then expected to improve the prognosis. We undertook a prospective screening using a competitive PCR in blood in 32 stem-cell transplant recipients. The sampling covered the first 150 days post-transplant, at days 21, 30, 45, 60, 90, 120, and 150. Twenty-four patients had anti-toxoplasma antibodies before transplant. Three of them (12.5%) had transient PCR-positive samples at 21, 45, and 90 days post-transplant, respectively. The three PCR-positive patients were febrile but had no funduscopic examination or cerebral computerised tomography (CT) scan abnormalities. The PCR signal disappeared when the patients were given trimethoprim-sulfamethoxazole, and no full-blown toxoplasmosis was observed. Toxoplasma reactivation evidenced using PCR is frequent in seropositive patients not receiving trimethoprim-sulfamethoxazole during the 1-3 months post-transplant. Toxoplasma PCR should be included in the diagnostic strategy of fever of unexplained origin in allogeneic stem-cell transplant recipients. Then, prompt specific therapy can be initiated to avoid development of full-blown toxoplasmosis.