Statement of Problem: The timing and pattern of eruption of second molars are clinically important factors and might be related to different types of craniofacial skeletal morphology and  malocclusion.Purpose: In this cross sectional study the eruptive positions of the second molars in Class I and Class II malocclusion were studied and compared.Materials and Method: Pretreatment   records including clinical examinations, and radiographs of 99 orthodontic patients, (56 girls and 43 boys with the mean age of 10.2 years) were evaluated. Approximately 25.3 % of the patients had skeletal Class I, 35.3% had skeletal maxillary Class II, and 39.3% had skeletal mandibular Class II malocclusions. The eruptive position in relation to a reference line, as well as, the developmental stages of the patients’ second molars, and the dental ages were recorded using theirs panoramic radiographs. Data were analyzed using ANOVA and Chi- square tests.  Results: The mean values of dental and chronologic ages of the subjects were similar. The distribution of various developmental stages in each malocclusion group was similar. There was an association between the type of skeletal malocclusion and dental developmental stage of the second molars ( p <0.0001). The eruptive position of second molars was more occlusal in the  maxilla of patients with  maxillary Class II and more apical in the mandible of patients with mandibular Class II ( p <0.0001) .Conclusion: According to the present study, the maxillary second molars erupt earlier in maxillary Class II malocclusion patients, and the mandibular second molars erupt later in mandibular Class II  malocclusion compared to other malocclusions.Key words: Malocclusion, Eruption, Molar, Skeletal, Class I, Class II