Background: Probiotic products are used to improve health, cure disease and in a prophylactic aim. However, there is limited research about its general effects on health in children, especially on oral health.  Aim: This study aimed to evaluate potential effects on oral health and otitis in 3-year- old children consuming probiotic Lactobacillus reuteri 17938 and Lactobacillus reuteri 5289.  Methods: This was a quantitative cross-sectional study where questionnaires concerning health and lifestyle of children (n=169) participating in the longitudinal study NorthPop Child, at the age of 4, 9, 18 and 36 months old, were compared to clinical parameters from a visit at the Public Dental Health Care at 3 years of age. Saliva samples from 142 children were analyzed by PCR. Results: This study showed that children consuming Lactobacillus reuteri 17938, had prevalence of the bacteria in saliva. Prevalence of Lactobacillus reuteri 5289 in saliva was not indicated. The prevalence of caries disease tended to be lower in probiotic- consuming children, though not statistically significant. Children consuming probiotics showed a higher prevalence of otitis and consumption of antibiotics compared to non- eaters.  Conclusion: Any conclusions about consumption and frequency required to gain and maintain the bacteria in the oral microbiome could not be made. Contradictory to other studies, this study found that children who consumed probiotics had more occasions of otitis media and antibiotic use. Future studies with a higher number of participants would be of interest to confirm these potential findings.