BACKGROUND: Children with disabilities may be particularly vulnerable to malnutrition, as a result of exclusions and feeding difficulties. However, there is limited evidence currently available on this subject. METHODS: A population-based case-control study was conducted in Turkana County, Kenya, between July and August 2013. Key informants in the community identified children aged 6 months to 10 years who they believed may have a disability. These children were screened by a questionnaire (UNICEF-Washington Group) and assessed by a paediatrician to confirm whether they had a disability and the type. Two controls without disabilities were selected per case: A sibling control (sibling nearest in age) and a neighbourhood control (nearest neighbour within one year of age). The caregiver completed a questionnaire on behalf of the child (e.g. information on feeding, poverty, illness, education), and anthropometric measures were taken. We undertook multivariable logistic and linear regression analyses to estimate the relationship between disability and malnutrition. RESULTS: The study included 311 cases with disabilities, 196 sibling controls and 300 neighbour controls. Children with disabilities were more likely to report a range of feeding difficulties. They were 1.6-2.9 times more likely to have malnutrition in comparison to neighbour controls or family controls, including general malnutrition (low weight for age), stunting (low height for age), low body mass index (BMI) or low mid upper arm circumference (MUAC) for age. Children with disabilities were almost twice as likely to have wasting (low weight for height) in comparison to neighbour controls (OR = 1.9, 95% CI 1.1-3.2), but this difference was not apparent compared with siblings (OR = 1.5, 95% CI 0.8-2.7). Children with disabilities also faced other exclusions. For instance those aged 5+ were much more likely not to attend school than neighbour controls (OR = 8.5, 95% CI 4.3-16.9). CONCLUSIONS: Children with disabilities were particularly vulnerable to malnutrition, even within this area of food insecurity and widespread malnutrition. Efforts need to be made to include children with disabilities within food supplementation programmes, and school based programmes alone may be inadequate to meet this need. Exclusion of children with disabilities from education is also a priority area to be addressed.