The extent and importance of genotype heterogeneity of Pneumocystis carinii f. sp. hominis within lungs have not previously been investigated. Two hundred forty PCR clones obtained from respiratory specimens and lung segments from three patients with fatal P. carinii pneumonia were investigated to detect genetic diversity in the internal transcribed spacer (ITS) region of the nuclear rRNA operon, the mitochondrial large-subunit (mtLSU) rRNA gene, and the dihydropteroate synthase-encoding gene. For two of the three examined patients, a mixture of different mtLSU rRNA and ITS genotypes was observed. Not all genotypes present in the lungs at autopsy were detected in the diagnostic respiratory samples. Compartmentalization of specific ITS and mtLSU rRNA sequence types was observed in different lung segments. In conclusion, the interpretation of genotype data and in particular ITS sequence types in the assessment of epidemiological questions should be cautious since genotyping done on respiratory samples cannot a priori be assumed to represent all genotypes present within the lung.The interpretation of molecular typing results in epidemiological studies of Pneumocystis carinii is complicated by the existence of coinfections. Several studies have reported coinfection with more than one genotype present in specimens from single patients (5). However, the majority of studies have relied on DNA extraction from diagnostic respiratory samples, which yield only a limited number of organisms. Very little is known of the dynamics of genotypes within the lungs, and whether genotype variation could result from compartmentalization of genotypes within the lungs has not previously been investigated.To address these questions, we studied polymorphisms at three genetic loci by a detailed investigation of DNA obtained from different segments of autopsy lungs. The mitochondrial large-subunit (mtLSU) rRNA and internal transcribed spacer (ITS) loci were chosen for analysis since these genes are genes most frequently used for genotype analysis and the dihydropteroate synthase (DHPS) locus, the target of sulfone and sulfonamide drugs, was chosen because of its association with sulfa resistance (9, 16).Specimens were obtained at diagnosis and postmortem from three patients who died of P. carinii pneumonia (PCP) between 1994 and 1997. PCP was diagnosed by microscopy and confirmed by histology at autopsy. Two patients with AIDS were included. Patient AIDS-1 was a 56-year-old male who died after 3 days of therapy, and patient AIDS-2 was a 45-year-old male who died after 17 days of therapy. Patient HL (age, 31 years) had a recurrence of Hodgkin's lymphoma and died 14 days after diagnosis of PCP.After autopsy the whole right lungs from patients AIDS-1 and AIDS-2 were stored at Ϫ80°C. After thawing, five biopsies were cut from five different areas of each lung. Two-by three-cm biopsies were selected from the apex and from the superficial and central areas of the middle lobe and from the base and central part of the inferior lobe of the right lu...