The degree of polymorphism and the allelic distribution of 2 major Plasmodium falciparum merozoite surface antigens (MSA1 and MSA2) have been analysed in clinical isolates from Colombia. DNA was prepared directly from patients' blood and used in PCR reactions to amplify block 2 of MSA1 and the central region from MSA2. Thirty one samples were analysed and a marked degree of length polymorphism was detected, especially for MSA2. A high proportion of multiple bands was also observed, most probably resulting from mixed infections. Allele-specific oligonucleotides were used to type both alleles. For MSA1, 26 out of 31 clinical isolates were of the RO33 type, 15 were MAD20 and three were typed as KI. When the MSA2 allele was analysed, 7 isolates hybridised with a CAMP specific probe and 6 hybridised strongly with an FC27-derived oligonucleotide. Two samples, which showed multiple bands, hybridised with both probes. Interestingly, in 14 out of 27 isolates the MSA2 allele remained unassigned by the specific probes. Five of these were cloned and their DNA sequenced; these sequences are discussed.