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In the HAART era, Pneumocystis jirovecii Pneumonia (PJP) continues to be a major opportunistic infection. PJ PCR is increasingly available to support the diagnosis of PJP. A ‘low level’ PCR result may represent PJ colonisation or a poor-quality specimen. Upper airway samples such as throat swabs (T/S) are also more likely to yield a negative or low level positive.Retrospective review of all HIV-infected adults with respiratory tract PCR-confirmed PJP and pneumonia over an 18 month period. Demographics, clinical features, management, clinical outcome and laboratory parameters were recorded.4/12 patients had negative T/S PJP PCR test before the diagnosis was confirmed. The mean cycle threshold (CT) value for throat swabs was 34.04. The mean CT value for sputum was 32.05.PJP PCR is a useful investigation. PCR will detect more cases than traditional tests (direct organism visualisation). This leads to earlier PJP treatment and earlier screening for HIV. While there is a trend towards lower CT value results in sputum when compared with throat swabs, any positive PJP result should trigger the offer of a HIV test. Patients with a negative URT PCR and clinical suspicion of PJP should receive empiric treatment and where appropriate proceed to BAL, as per national guidance.