Childhood undernutrition is a global public health challenge, affecting children unevenly within the same household. This study assessed the behavioural and genetic correlates of malnutrition among children aged 1–3 years in a district of the Greater Accra Region, Ghana. A cross-sectional study involving 262 child-caregiver pairs was conducted. Children were classified as wasted, stunted or healthy based on anthropometric indices. Feeding behaviours - including appetite, food refusal, force-feeding, and maternal feeding anxiety were assessed using the International Complementary Feeding Evaluation Tool. Saliva samples were used to genotype nine single nucleotide polymorphisms (SNPs) associated with appetite and energy regulation, and a polygenic risk score (PGRS) was generated. Wasted children had significantly lower appetite z-scores (Mean difference MD (Confidence interval CI)): -0.37 (-0.65, -0.09) and higher z-scores for food refusal (0.30 (0.03, 0.58)) and caregiver feeding anxiety (0.67 (0.39, 0.94)) compared to healthy children. Maternal feeding anxiety attenuated the association between appetite and WHZ while remaining a strong independent predictor. No associations were found between feeding behaviour and stunting. Although force-feeding was common (33% of children), it did not differ by nutritional status. The SNP rs2274333, showed a higher frequency of homozygosity for the AA genotype in wasted children. The PGRS was significantly associated with low appetite (p=0.046) but not with food refusal or nutritional status. Children with wasting had a lower appetite and a higher food refusal. This is associated with high levels of maternal feeding anxiety, but does not seem to have a strong genetic basis.