Molecular methods such as qPCR have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of Interspace regions length between 16S and 23s ribosomal DNA, that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro in 66 samples sent in for routine bacterial diagnostics. The samples derived from patients with infections of normally sterile sites (without a resident microbiota). Results were identical in 20 (30%) of samples, IS-pro detected more bacterial species than culture in 31 (47%) of samples, and five of the ten culture negative samples were positive with IS-pro. The case histories of the five patients from which these culture negative/IS-pro positive samples derived, suggest that the IS-pro findings were highly clinically relevant. Our findings indicate that an open molecular approach such as IS-pro may have a high added value for clinical practice.