Undernutrition is a global health concern, particularly in low-income countries, and can manifest as wasting, stunting and/or underweight. In Yemen, the recent armed conflict is likely to have significantly increased the incidence of undernutrition in young children, particularly those living in communities that were already experiencing socioeconomic and health disparities. To explore the risk factors associated with wasting, stunting and underweight in children aged between six months and five years living in one district of Yemen. A cross-sectional study was conducted using a two-part questionnaire to collect anthropometric measurements and sociodemographic characteristics of children enrolled on an outpatient programme for undernourished children at three healthcare facilities in the Jiblah district, and of their families and households. Of the 120 children included in the study, 58 (48%) had wasting, 27 (23%) had stunting and 35 (29%) were underweight. Risk factors for undernutrition included being under the age of three years, being a girl, having had a low birthweight, having siblings under the age of five years, having a mother who is a housewife, living in a household relying on unimproved sources of drinking water, living in a rural area, and living in a low-income household. The nutritional status of children in Yemen is under continuing threat. The identification of risk factors for undernutrition may increase awareness of the issue and influence the policy decisions of the international community.