Genetic diversity of the merozoite surface antigen-2 gene of the human malaria parasite Plasmodium falciparum has been analyzed in a Senegalese village where malaria is holoendemic. A cross-sectional survey of 65 residents was performed in 1992 during the high transmission season. Plasmodium falciparum was detected both by microscopy (77% positive samples) and DNA amplification using a single (29% or 38% positive samples, depending on the primers used) or nested polymerase chain reaction (PCR) (78% positive samples). The overlap between the positive nested PCR and microscopic examination was not complete. The PCR fragments were analyzed for size polymorphism on agarose gels, and were subsequently assigned to the major allelic families 3D7 or FC27 by hybridization with family-specific probes. Both allelic families were found, with a slightly higher prevalence for FC27. Chimeric alleles that failed to hybridize under stringent conditions to the reference probes were also observed. Some were typed using a novel PCR approach, using hybrid pairs of primers, consisting of a family-specific sense oligonucleotide combined with an antisense oligonucleotide specific for the other family. Combining typing techniques, 82% of the positive PCR results yielded more than one band. Both the overall number of fragments and the number of allelic types per carrier were markedly reduced around the age of 15 years. The number of DNA fragments decreased abruptly from an average of four per carrier before the age of 15 years to an average of two in individuals more than 15 years of age.(ABSTRACT TRUNCATED AT 250 WORDS)