The diagnosis of toxoplasmosis in congenitally infected children or in immunocompromised patients can be difficult; serology is not reliable, and the diagnosis must be based on the combination of symptomatology and the direct demonstration of the parasite in clinical specimens by microscopy, antigen detection, or inoculation of samples into mice or tissue cultures. These techniques are either insensitive or time-consuming. To determine the value of the polymerase chain reaction (PCR) for the diagnosis of Toxoplasma gondii infections, we compared this technique with conventional detection techniques, such as microscopy, tissue culturing, and mouse inoculation. We were able to detect T. gondii by PCR in clinical specimens and tissue samples that were obtained postmortem from a bone marrow recipient with cerebral toxoplasmosis and from three congenitally infected children. The presence of T. gondii was demonstrated in brain tissue, cerebrospinal fluid, the heart, and skeletal muscle tested fresh or after fixation in Formalin. In only one sample was T. gondii isolated by mouse inoculation but not detected by PCR. Because it is a sensitive, relatively rapid, and specific method and because it can be applied to a variety of different clinical samples, PCR can be considered a valuable additional tool for the identification of T. gondii infections.