Background The GeneXpert® MRSA/SA SSTI test allows early detection of methicillin-resistant staphylococci in intraoperative samples of prosthetic joint infections (PJI) in order to stop early broad-spectrum antibiotics. Questions/Purpose (1) What is the rate of false-negative GeneXpert® MRSA/SA SSTI test results? (2) Does a false-negative GeneXpert® MRSA/SA SSTI test result increase the risk of treatment failure for the patient with a PJI? (3) What are the risk factors of a false-negative result? Method A retrospective study was carried out to compare all GeneXpert® assays to conventional cultures in prosthetic joint infections from April 1st, 2012 to October 1st, 2016. False-negative (FN) results (absence of methicillin-resistant staphylococci (MRS) with GeneXpert® test, but presence in the culture) were identified. We compared the rate of treatment failure between FN results and other test results and we established the risk factors of having a FN result. Results Among the 612 GeneXpert® results, the rate of FN results was 3.6 % (22/612). We found a significant increase in treatment failures for prosthetic joint infection with a FN result with 14 treatment failures (14/22) compared to 198 treatment failures (198/590) in the other test results (OR, 2.1; 95 % CI, 1.3-3.4, p = 0.0019). Not considering suppressive antibiotics as a treatment failure, we found no significant difference in the rate of treatment failures between the false-negative tests and the other tests (OR, 1.36; 95 % CI, 0.66-2.81, p = 0.41). Tobacco use (OR, 3.8; 95 % CI, 1.4-10.3, p = 0.004), ASA classification (OR, 2,4; 95 % CI, 0.9-6.9, p = 0.064), history of infection in the joint (OR, 3.2; 95 % CI, 1.2-9.6, p = 0.007), chronic infections (OR, 3.2; 95 % CI, 0.8-17.5, p = 0.01) and polymicrobial infections (OR, 3.2; 95 % CI, 1.1-9.2, p < 0.0001) were risk factors for a FN result. Conclusion GeneXpert® tests in prosthetic joint infections showed a low rate of FN results. An increased risk of treatment failures was observed in FN results only when long-term use of suppressive antibiotics was considered as treatment failure.