Background Birth polymerase chain reaction (PCR) testing improves early detection of HIV and allows for early treatment initiation. National guidelines exist, but it is unknown whether these are being implemented correctly. Objectives To determine whether HIV-exposed infants at the Mangaung University Community Partnership Programme Community Health Centre (MUCPP CHC) received PCR tests at birth, if HIV-positive infants were initiated on treatment, if follow-up dates were scheduled and the percentage of mothers or caregivers who returned to collect the results. Methods The study was a retrospective descriptive file audit (1304 files) of births from 01 January to 31 December 2016 at MUCPP CHC. The study sample was 428 infants born to HIV-positive mothers. The birth register was used to collect the infants’ HIV PCR test barcodes. The birth and 10-week PCR results were retrieved from an electronic database at the Virology Department, University of the Free State. Results In total, 375 infants received a birth PCR test (87.6%) of which 4 (1.1%) tested HIV positive and 327 (87.2%) negative. Follow-up tests were not scheduled. However, 145 (44.3%) HIV-negative infants returned for a 10-week test. Irrespective of the PCR birth result, 157 (36.7%) infants were brought for a 10-week follow-up test at which time 3 (1.9%) tested positive and 151 (96.2%) negative. Conclusion The majority of HIV-exposed infants received a PCR test at birth; however, the clinic is below the national target (90%) for HIV testing. A record-keeping system of infants’ visits does not exist at MUCPP CHC, making it impossible to determine whether HIV-positive infants were started on antiretroviral treatment.