A "nested" PCR approach with primers based on conserved plasmid sequences was used for the highly sensitive and specific detection of Coxiella (C.) burnetii in clinical samples collected from cattle, dogs, cats and humans. Results were in good agreement with those obtained from Capture-ELISA and isolation of the organism in BGM cell culture. We also tested primers with sequences derived from genomic DNA and sequences based on 16S rRNA. In addition, we applied PCR for the differentiation of C. burnetii plasmid types from 28 isolates originating from the USA, Europe and South Africa. Reference isolates Nine Mile RSA493, Dugway 5J108-111 and all European isolates tested were recognized only by primers specific for the QpH1 plasmid. One isolate from a goat abortion in Namibia reacted identically to the reference isolate Priscilla Q177 bearing the QpRS plasmid. Reference isolate S Q217 with plasmid sequences integrated into the genome reacted with none of the plasmid-specific primer pairs.