SummaryPolymorphisms of the haptoglobin (HP) gene and deletions in α-globin gene (α-thalassaemia) are common in malaria-endemic Africa. The same region also has high incidence rates for childhood acute seizures. The haptoglobin HP2-2 genotype has been associated with idiopathic generalized epilepsies and altered iron metabolism in children with α-thalassaemia can potentially interfere with neurotransmission and increase the risk of seizures. We investigated the hypothesis that the HP2-2 genotype and the common African α-globin gene deletions are associated with the increased risk of seizures. 288 children aged 3–156 months admitted with acute seizures to Kilifi District Hospital (Kenya), were matched for ethnicity to an equal number of community controls. The proportion of cases (72/288 [25.0%]) and controls (80/288 [27.8%]) with HP2-2 genotype was similar, p = 0.499. The allele frequency of HP2 gene in cases (49.3%) and controls (48.6%) was also similar, p = 0.814. Similarly, we found no significant difference between the proportion of cases (177/267 [66.3%]) and controls (186/267 [69.7%]) with deletions in α-globin gene (p = 0.403). Among cases, HP2-2 polymorphism and deletions in α-globin gene were neither associated with changes in the type, number or duration of seizures nor did they affect outcome. We conclude that the HP2-2 polymorphism and deletions in α-globin gene are not risk factors for acute seizures in children. Future studies should examine other susceptibility genes.