The genome of Plasmodium falciparum has an A/T content of around 81%. This, together with a high cysteine content and the high molecular weight of several proteins, make the expression of recombinant parasite proteins in heterologous systems challenging. P. falciparum erythrocyte membrane protein 1 (PfEMP1) is a family of proteins composed of several Duffy-binding like (DBL) and cysteine-rich inter-domain region (CIDR) domains involved in cytoadhesion to human host receptors and development of severe malaria. Expression of correctly folded single- and multiple-domain PfEMP1 fragment regions containing cysteines forming disulfide bonds, remains particularly difficult. Nevertheless, expression of single DBL and CIDR domains has been successful and this protocol describes the expression and purification of single-domain soluble PfEMP1 fragments using the Escherichia coli SHuffle expression system.