The presence of P. carinii DNA in serum and in Peripheral Blood Mononuclear Cells (PBMC) during acute phase of PCP in AIDS patients was previously demonstrated by several authors using different specific primers. Amplification by ITSs nested PCR followed by TSO hybridization of P. carinii isolates derived from BAL and blood samples allows to compare genotypes involved in the disease and genotype-related dynamics of Pc-DNA clearance from blood during therapy. Different virulence characteristics among P. carinii genotypes could explain the various spectrum of clinical presentation (pulmonary and extrapulmonary) and susceptibility to classic antipneumocystic drugs during PCP.