Diagnosis of infection after total hip replacement is known to be difficult. Isolation of the bacterial pathogen can give false negative results with current culture methods. Molecular-based methods, as Polymerase Chain Reaction (PCR), may help detect bacteria where culture fails; however, contamination with bacterial DNA when using universal bacterial primers has for a long time been a recognized problem. In this study we describe our attempts of designing a new, rapid PCR method for detection of bacteria in synovial fluid. During the development of this method both the QIAamp® DNA Mini Kit and the MagNA Pure LC Microbiology Kit MGRADE was tested for its extraction reliability.Hundred and fifteen synovial fluid samples were analysed for Staphylococcus aureus and methicillin-resistant staphylococci DNA, using the nuc and mecA gene respectively. The synovial fluids were also tested with universal bacterial primers and probe. The PCR results were then compared to the standard culture results.This study shows that culture for S.aureus and methicillin-resistant staphylococci was concordant with the results for nuc and mecA PCR. The universal PCR protocol detects more bacteria (58%) than the culturing method, but also presents many inconclusive results difficult to interpret. In our protocol the MagNA Pure LC Microbiology Kit MGRADE showed to be more reliable as DNA-extraction method. Our goal in this study was to develop a better and more reliable diagnostic method for the complicated hip replacement infections. The protocol shows the high potentials of the molecular-based methods, but the bacterial DNA contamination issues using broad-range PCR still remain a problem, and more research is needed to overcome this obstacle.