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Background Though birth interval has beneficial effects on health status of the mother and their children, it is affected by range of factors some of which are rooted in social and cultural norms and the reproductive behaviors of individual women. However, there was limited data showed the determinants of birth intervals in rural pastoral communities of South Ethiopia. Therefore, the study was aimed to assess the determinants of inter birth interval among women’s of child bearing age in Yaballo Woreda, Borena zone, Oromia Regional State, Ethiopia. Methods A community based unmatched case–control study with multi stage sampling technique was conducted from January to March 2012. Cases were women with two subsequent birth intervals of less than three years and controls were women with two subsequent birth intervals between three and above years. Simple random sampling technique was employed to select six hundred fifty two (326 cases and 326 controls) study subjects. All explanatory variables that were associated with the outcome variable (birth interval) during bivariate analysis were included in the final logistic model. Multivariable backward logistic regression when P values less than or equal to 0.05 and 95% CI were used to determine independent determinants for the outcome of interest. Results The median duration of birth interval was 31 & 40 months among cases and controls respectively. Variables such as number of children (AOR 3.73 95% CI: (1.50, 9.25), use of modern contraceptives (AOR 5.91 95% CI: (4.02, 8.69), mothers’ educational status (AOR 1.89 95% CI: (1.15, 3.37), and sex of the child (AOR 1.72 95% CI: (1.17, 2.52) were significantly associated with birth intervals. Conclusions Concerted efforts to encourage modern contraceptive use, women education, and breastfeeding should be made.