We have developed a highly sensitive microbial analytical system, the Yakult Intestinal Flora-SCAN (YIF-SCAN), based on reverse transcription-quantitative PCR, to quantify the intestinal microbiota. Targeting ribosomal RNA “molecules,” which are present in abundant copies in the microorganisms, YIF-SCAN is at least hundreds of times more sensitive (detection limits: 102-3 cells/g feces, 1 cell/mL blood) than conventional DNA-based methods, and hence enables highly sensitive and precise detection of viable microorganisms in various types of samples, such as stools, blood etc. Specifically, this high analytical sensitivity enables more accurate and reliable detection (compared with conventional culture methods) of microorganisms migrating in the blood, bacteremia, in patients with different diseases such as pediatric patients with febrile neutropenia, neonates with clinically diagnosed sepsis, and patients with type 2 diabetes mellitus or ischemic stroke. Such detection of bacteremia during gastrointestinal surgery can also be particularly effective for preventing postoperative infectious complications. Herein, we review some of the studies corroborating the potential application and clinical significance of YIF-SCAN in diagnosing bacteremia (even at marginable levels) in patients with different diseases.