Introduction: Microbiota in healthy individuals includes many and different microorganisms. Infections, use of antibiotics, various chemicals (antiseptic solutions, soaps, shampoos, etc.) can change the human microbiota. This study was planned to compare the effect of wiping bath with 2% daily chlorhexidine gluconate and soap-free body washing solution on the skin microbiota of the patients hospitalized in the pediatric intensive care unit. Methods: The research was carried out as a randomized controlled experimental study with 60 children hospitalized in the pediatric intensive care unit of a training and research hospital in February 2021-January 2022. In the study, the children in group I (n=30) were given a wiping bath with 2% chlorhexidine gluconate, which is the routine application of the unit and the children in group II (n=30) were given a soap-free body wash solution. In both groups, swab samples were taken from the armpits and groin for 3 days just before the application of the wiping bath and 6 hours after the application of the wiping bath. Results Children participating in the study 36.7% (n=22) were girls and 63.3% (n=38) were boys. The mean age of the participants was determined as 6.05±5.04. When the reproductive changes in the permanent skin flora between the groups were examined, a significant difference was found between group I and group II before and after bathing on the 1st, 2nd and 3rd days (p=0.001). Persistent skin flora decreased significantly in group I on the 1st day, while it disappeared completely on the 2nd and 3rd days. In group II, the permanent skin flora continued to be preserved for 3 days. Conclusion: As a result of the research, it was determined that 2% chlorhexidine gluconate wiping bath in children hospitalized in the PICU significantly reduced the persistent skin flora in the armpits and groin.