Background: P. falciparum pathogenesis is attributed to its ability to evade the human immune system by modifying infected host red blood cells to adhere to the vascular endothelium. The main antigenic ligands responsible for both cytoadherence and antigenic variation are members of the P.falciparum Erythrocyte Membrane Protein-1(PfEMP1)family. Therefore, PfEMP1 is considered a key player in the pathogenicity of P. falciparum. The aims of this study is to identify subtypes of CIDRα1 domain variants expressed frequently by parasites in order to understand causes of severity of malaria in <5years children. Methods: A hospital based cross sectional study was conducted in which patients presenting with severe malaria were recruited. Patients’ demographic data plus severe malaria syndromes were measured. RNA was extracted from parasitized blood samples using Trizol method. qPCR was performed for the quantification and identification of PfEMP1 var genes expression using CIDRa1 subtypes specific primers and control genes. Results: Of all CIDRα1 variants gene subtypes: CIDRα1, CIDRα1DC8, CIDRα1A (group B/A) and CIDRα1.4, CIDRα1.5b and CIDRα1.7 (group A) were transcribed most frequently at higher levels in severe malaria in under 5 years children compared to uncomplicated malaria. Conclusion: PfEMP1 CIDRα1 subtypes: CIDRα1.1in DC8 and CIDRα1A, CIDRα1.8a, CIDRα1.4, CIDRα1.5b and CIDRα1.7 in DC13 are highly are associated with severe childhood malaria. Further studies to establish the specific role of CIDRα1 subtypes in severe malaria are important to inform on effective vaccine development. Keywords: CIDRα1, Hyperparasitemia, PfEMP1, Tanzania