Nosocomial infection (NI) increased the rate of mortality, morbidity and financial load for patients and Healthcare Facilities (HFs). Regarding to many advances in controlling NIs, it is still a worldwide problem. Layout of HF (department configuration) has a vital role in controlling NIs, because the pathogen microorganisms can transmit among departments. Some departments can transmit microorganisms much more than the other departments, called cause, and some of them received the microorganisms more than the others, called effect. Both are risky.This study attempts to propose a comprehensive algorithm for selecting low risky department(s) for upgrading of HFs by use of Multiple Criteria Decision-Making (MCDM) methods.Among MCDM methods, this study has hybrid WSM and Expanded DEMATEL, beside modified Nominal Group Technique to minimize NIs risk in upgrading of HFs. The resulted decision-making algorithm is validated by implementing in a HF as a case study.The final proposed algorithm and the resulted low risky departments are approved by head and manager of the HF. Therefore, the algorithm is valid, and the feasibility of algorithm is approved by achieving the result from implementing of algorithm in the case study.To conclude, the proposed algorithm can be a solution to minimize the risks of NIs, while upgrading, in each HFs and make the decision of HF's managers easier and logic.