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Background: Human Immunodeficiency Virus greatly affects young peoples in developing countries, of which sexual transmission is the major route including vaginal, oral and anal sex. Understanding the full range of sexual behavior among young people, especially oral and anal sexual experience is very crucial to design appropriate intervention strategies. This study was to assess oral and anal sexual experience and associated factors among preparatory school youths in Dire Dawa city, Eastern Ethiopia. Methods: School based cross sectional study was conducted among 1067 school youths attending preparatory school. Systematic random sampling method was used to select study participants. Data were collected using self-administered questionnaire and entered in to Epi-data version 3.3.1 and exported to SPSS 20 for analysis. Descriptive and bivariate logistic regression was done. Variables in bivariate analysis with P< 0.25 were entered to multiple bivariate logistic regression analysis to determine predictor variables. P < 0.05 was declared as statistically significance and AOR with 95% CI used to assess strength of association. Results: The proportion of youths who reported having oral sex was 9% (88) and that of anal sex was 6.7% (66). Having multiple sexual partners was reported by 65.8% and 56.5% of youths who ever engaged in oral and anal sex respectively. From those who ever engaged to oral sex and anal sex 15.9% and 34.8% consistently used condom respectively. Oral sex practice was significantly associated with intimate partner ever engaged to oral sex practice (AOR = 4.53, 95% CI: 2.26–9.05), ever engaged to vaginal sex (AOR = 16.38, 95% CI: 7.22–37.19), older age (20-24years) (AOR = 2.45, 95% CI: 1.24–4.86), ever drinking alcohol (AOR = 2.11,95% CI:1.02–4.34), and ever smoke shisha (AOR = 2.85,95% CI:1.4–5.83). Similarly anal sex experience was significantly associated with intimate partner ever engaged to anal sex (AOR = 5.34, 95% CI: 4.2–26.98), ever engaged to vaginal sex (AOR = 10.64, 95% CI: 2.39–11.9), ever watching pornographic movies (AOR = 3.86, 95% CI: 1.45–10.29) and parental monitoring of youth’s sexual behavior (AOR = 2.63, 95% CI: 1.12–6.19). Conclusions: Significant proportion of youths had engaged in oral and anal sexual practice and multiple sexual partners were common among youths for oral and anal sex. In the contrary consistent condom use was very poor. A combination of sexual health education intervention strategies should be implemented at family, school and community level. [ABSTRACT FROM AUTHOR]