BackgroundImmunization coverage in Ethiopia is less than the herd immunity level desired to prevent the spread of eight target diseases targeted by the World Health Organization’s Expanded Program of Immunization. In particular, the Somali region of the country still has by far the lowest level of immunization coverage. The objective of this study was to measure the immunization coverage of 12–23 months old children and associated factors in the urban and rural areas of Jigjiga district.MethodsA community based cross-sectional survey was conducted in 582 households with 12–23 months old children in two urban and four rural wards. The data were collected from mothers or caregivers through interviews based on pre-tested and structured questionnaires and from the review of vaccination cards. Data were processed using SPSS version 16. To identify factors associated with the immunization status of children, bivariate and multiple logistic regression analyses were worked out and the Hoshmer and Lemeshow’s goodness-of-fit was used to assess the fitness of multiple logistic regression model.ResultsThree–fourth (74.6%) of the children surveyed were ever vaccinated, whereas 36.6% were fully vaccinated. The immunization coverage rate from card assessment for Bacillus Calmette-Guérin was 41.8%, while for Oral Polio Vaccine Zero, Oral Polio Vaccine One /Pentavalent1, Oral Polio Vaccine Two /Pentavalent2, Oral Polio Vaccine Three /Pentavalent3, and measles were 10.4%, 41.1%, 33.9%, 27.5%, and 24.9%, respectively. Maternal literacy (AOR = 3.06, 95% CI = 1.64, 5.71), Tetanus Toxoid Vaccine (AOR = 2.43, 95% CI = 1.56, 3.77), place of delivery (AOR = 2.02, 95% CI = 1.24, 3.28), place of residence (AOR = 2.04, 95% CI = 1.33, 3.13), and household visits by health workers (AOR = 1.92, 95% CI = 1.17, 3.16), were found to be factors significantly associated with full immunization in the multivariate logistic regression analysis.ConclusionsThe overall immunization coverage was found to be low. Hence, to increase the immunization coverage and reduce the incidences of missed opportunity, delivery in the health institution should be promoted, the outreach activities of the health institutions should be strengthened and greater utilization of health services by mothers should be encouraged.