BACKGROUND To reveal the characteristics of genotype and phenotype of HIV strains in blood and some tissues of AIDS patients. METHODS The virus was isolated from peripheral blood mononuclear cell (PBMC),cerebrospinal fluid (CSF)and lymph nodes of 3 AIDS patients by coculture with PBMC stimulated by PHA for 72 hours from uninfected donor. The cytopathic effect of the HIV isolates was determined in cultured MT2 cell line. The env gene sequences form proviral DNA were analyzed by GCG software. RESULTS In one patient,there were differences between the strains from blood and different tissues both in genotype and phenotype. The biological phenotypes of two strains from CSF were non syncytium (NSI) type, their env sequences were similar to standard CNS tropic strain (SF162). CONCLUSIONS The viral heterogeneity exists in different body compartments within an infected individual. The neurotropic isolate which is similar to international standard strain exists in some AIDS patients in China.