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Aim Study aims were to determine the most effective chlorhexidine concentration to be used in reducing microbial colonization in patients under mechanical ventilation and to examine the effect of oral care using different concentrations on the integrity of the oral mucous membranes. Design This research was a randomized controlled double‐blinded experimental study. Method The sample of study consisted of the 116 adult patients who remained intubated. Oral care was given to patients 4 times/day as per nurse protocol. Every morning during for 4 days, the intraoral mucosa of all groups of patients was assessed. Microbial colonization samples from oral mucosa were taken in the morning before oral care. A determination of the species of microorganisms in these samples was made. Results A statistically significant difference was found with regard to the reproduction of microorganisms between the oral mucosa samples taken from patients using 2% and 1% chlorhexidine solutions (P < 0.001). In the cultures taken from patients on the first and fourth days of intubation, a total of 36 different microorganisms were seen to be reproducing. Conclusion It was concluded that the most effective oral solution for the prevention of microbial colonization in patients under mechanical ventilation was chlorhexidine 1%.