The implementation of widespread unselected screening for Neisseria gonorrhoeae in England, using nucleic acid amplification tests (NAATs), has raised concerns regarding the potential increase in misdiagnoses. To increase the positive predictive value, confirmatory testing of positive specimens has been recommended; however, in practice this can be difficult to perform. This study examined the role of two different testing strategies for confirming the N. gonorrhoeae status of specimens that had been examined by the ProbeTec Strand Displacement Amplification (SDA) assay (Becton Dickinson). A total of 227 residual clinical specimens in SDA assay collection tubes were sent for confirmatory testing using two different testing approaches: (i) examination using two in-house real-time PCR assays (opa and porA pseudogene) and (ii) examination using the APTIMA Combo 2 (AC2) assay and the APTIMA Monospecific N. gonorrhoeae (AGC) tests (Gen-Probe). Of the 113 SDA-positive specimens (including low positives) examined, 93 % were confirmed as N. gonorrhoeae-positive using either one or both real-time PCR assays. In contrast, only 34 % were confirmed using the AC2 and/or the AGC assays. All 114 SDA-negative specimens were confirmed as negative using all four confirmatory tests. Clearly the AC2 and AGC assays cannot reliably be used to confirm residual specimens in SDA assay transportation buffers, due to the incompatibility of different platform chemistries. Although high rates of confirmation (93 %) can be achieved when examining residual SDA assay specimens using independent real-time PCR assays, establishing well-validated in-house real-time PCR assays for diagnostic use is a large undertaking for many primary laboratories and so such tests may be better confined to specialist laboratory services.