Highly polymorphic regions of the circumsporozoite protein (CSP) of Plasmodium falciparum are associated with cellular immune responses. One of these regions, the TH3R polymorfic region of the csp gene codes for known T-cell epitopes. The present study tested the use of SSCP to determine sequence variations of the TH3R regions of four clones of P. falciparum (3D7, HB3, Dd2 and K1) which are known to have different TH3R regions. Single-strand conformation polymorphism (SSCP) technique was performed on amplified products labelled with fluorescent primer (both strands) and electrophoresed in an automated sequencer. Various gel compositions and electrophoresis conditions were tested. Even if some electrophoretogram differences were observed between clones, they could not distinguish between the alleles.