In order to develop a practical approach for detection of Chlamydia pneumoniae by polymerase chain reaction (PCR) in clinical respiratory samples, positive controls for rDNA and major outer-membrane protein gene targets were constructed. Two PCR strategies detected chlamydial DNA in excess of 1000 copies per mi in the same 19 of 135 clinical specimens and identified PCR inhibitors in the same four samples. (C) 1999 Academic Press.