Background: For many infants and children non-nutritive sucking habits are very common and one of those habits is pacifier sucking, however, if this habit persist beyond the age of 3 years it may cause esthetic, occlusal and psychological changes. This study was conducted to determine the effect of pacifier sucking habit on the oral health of children aged 1-5 years old in Baghdad city and to assess its role in the modification of the oral microflora. Materials and methods: The study was carried out among children aged 1-5 years old with no history of any systemic diseases nor taking any medical treatment for the past two weeks prior to the examination, 50 children with continuous pacifier sucking habit were chosen to be the study group, compared to 50 children without any sucking habit (control group) matching the study group in age and gender. Information sheet filled by the parents concerning general health and frequency of oral infections of their children was taken. Oral microorganisms samples were obtained from children and cultured aerobically using blood agar, MacConkey agar, chocolate agar and sabauraud, s dextrose agar. Results: Children with pacifier sucking habit showed higher frequency of having continuous oral infections (44%) whereas in non pacifier sucking group it was zero. Concerning the oral infections, a statistical difference was found by which the pacifier sucking children oral infections exceed significantly that of the non pacifier sucking children (P<0.01). Regarding the oral microorganisms, more types were found among pacifier sucking children. Candida, Sterp.pyogenes, strep.faecalis, E.coli, Acinetobacter and sterp. pneumonia were more common among pacifier sucking children. Conclusion: Pacifier use affect types and frequency of microorganisms found in the oral cavity which may affect the frequency of oral infections. Health programs should be constructed to improve parents' knowledge concerning the effect of pacifier use in the oral health of their children and how to clean it if it used to reduce its contamination.