The genotypes of Toxoplasma gondii strains isolated from HIV and non-HIV immunocompromised patients with cerebral and extracerebral toxoplasmosis were determined and compared to those of strains isolated from non-immunocompromised patients in order to identify the possible relationships between parasite genotype and morbidity of toxoplasmosis. One hundred and ten strains of T. gondii were obtained, either by cell culture (n = 73), brain biopsy (n = 17) or mouse inoculation (n = 20). Ninety strains isolated from immunocompromised patients (74 HIV+ and 16 non-HIV patients) were compared to 20 strains isolated from immunocompetent patients (17 cases of congenital toxoplasmosis, and three cases of primary acquired infection). Genotyping was performed by PCR/RFLP on locus SAG2, and T. gondii strains were classified as Type I, II or III. Ninety out of 110 strains were successfully genotyped, including 20 strains that had been maintained in mice, 69/73 strains maintained in cell cultures, but only 1/17 strains from formalin-fixed paraffin-embedded brain biopsies. 76.7% of the strains in the study population were of type II, 15.6% were type I and 7.7% were type III. The distribution of strain genotypes in immunocompromised and non-immunocompromised patients was comparable: 14.1% and 21% for type I, 76.1% and 79% for type II and 9.8% and 0% for type III, respectively; no correlation could be established between genotype and clinical presentation, i.e., cerebral or extracerebral toxoplasmosis. These results suggest that the type of infecting parasitic strain does not predominantly influence the pathogenesis of toxoplasmosis in immunocompromised patients and fully supports the need for specific prophylaxis in patients infected by T. gondii, regardless of the strain genotype.