Background
Malnutrition among children remains common in many parts of the world, particularly in developing countries. In Ethiopia, it is one of the most important health and welfare problems among infants and young children. Ethiopian Somali regional state is one of the most underserved regions in terms of access to essential services and characterized by a high level of child malnutrition, food insecurity, and vulnerable livelihoods. Therefore, the current study was undertaken to assess the magnitude and factors associated with malnutrition among children aged 6–59 months in Shinille Woreda, Ethiopian Somali regional state.

Methods
Community-based cross-sectional survey, involving 694 study participants selected by multistage sampling technique, was conducted in Shinile Woreda from February to March, 2014. Data were collected using structured questionnaire and anthropometric measurement. Anthropometric indices were calculated using ENA for SMART software 2011, and SPSS V.16 was used for data analysis. Associations were computed using the OR and 95 % CI. P-value less than 0.05 were considered as statistically significant.

Results
The overall prevalence of stunting, underweight and wasting were 33.4 %, 24.5 % and 20 %, respectively. The main associated factors of stunting and wasting were family size, child’s sex and monthly income of the households. Immunization status was the only variable associated with all forms of malnutrition. Non-immunized children were 2.5 times more likely become underweight than their counterparts. The prevalence of stunting was 3.8 times higher in households with large family size. Female children were 1.5 times more likely become wasted than their counterparts.

Conclusion
Prevalence of malnutrition among under five children in Shinile Woreda is still high. Our finding highlighted the importance of childhood vaccination, family planning and poverty alleviation as potential targets for intervention.