Microbiological tests are important for the diagnosis of infectious diseases and their follow-ups. Under the medical reimbursement system, Gram staining has been approved as a fast laboratory test for outpatients, and remuneration for the management of laboratory testing is also applied to it. On the other hand, a serious problem in conducting microbiological testing is unprofitability, including high personnel costs and expenses for reagents. We conducted a survey involving eight medical institutions of the costs for Gram staining, bacterial culture and identification, anaerobic culture, antimicrobial susceptibility testing, isolation culture of acid-fast bacteria, and testing for susceptibility to antimycobacterial agents. The mean costs for all these items were higher than medical service fees. Even after the previous revision of the medical fee and increases in service fees, the operations of the above-mentioned tests still remain unprofitable. The Japanese Promotion Council for Laboratory Testing has been involved in ensuring appropriate reimbursement of medical fees. The council conducted surveys and assessments of costs for laboratory tests and their clinical values, and submitted a request to the Ministry of Health, Labour and Welfare for an improvement in the medical treatment fees. In response to our request, there were increases in some medical service fees, including the increase from 170 to 400 yen for Gram staining. It is important to continue to ask relevant government agencies to ensure appropriate remuneration for microbiological testing based on objective data.