We describe fractionation of the Plasmodium falciparum genome into 14 chromosomal DNA molecules by pulsed-field gel electrophoresis. This number agrees with the number of chromosomes observed by electron microscopic visualization of kinetochores. The assignment of 25 markers to 12 of the 14 chromosomes in three cloned parasite lines demonstrates that chromosomal size variation can greatly change the relative migration of genetically equivalent chromosomes. Deletions that include genes for three different histidine-rich proteins, located on chromosomes 2, 8, and 13, contribute to size differences in some clones. Other karyotypic differences result from chromosome segregation and/or recombination during meiosis.The development of pulsed-field gel electrophoresis (PFG electrophoresis) for the fractionation of double-stranded DNA molecules in the megabase range (1) has enabled the study of chromosomes from organisms refractory to other approaches. The genome of Plasmodium falciparum was resolved into at least 7 (2-5) chromosomes in the earliest studies. Subsequently, at least 11 chromosomes were resolved (6) and hence the most recent estimate approximates the total of 14 chromosomes obtained by electron microscopic observation of kinetochores (7).The P. falciparum chromosomes are highly polymorphic in size, both in cultured isolates and in parasites obtained directly from patients (2-6). Although the karyotype of a cloned line is stable during the asexual cycle, some size variation occurs in vitro that may result from deletions of genes such as the knob-associated histidine-rich protein (KAHRP) gene (4,8). Other deletions may involve repetitive DNA (3). However, studies on the progeny from a genetic cross of two cloned isolates have shown that polymorphisms can arise during the cross (9), presumably from chromosomal rearrangements during sexual reproduction in the mosquito.A number of genes encoding malaria antigens currently viewed as candidate vaccine molecules have been assigned to different chromosomes (2-6, 8, 9). For example, the ringinfected erythrocyte surface antigen (RESA) gene is located on chromosome 1 (2, 4), the circumsporozoite protein (CSP) gene is located on chromosome 3 (9), and the gene encoding the precursor to the major merozoite surface protein (PM-MSA) is located on a larger chromosome (10). P. falciparum is haploid (9) and recombinant genotypes (that could include antigenically novel forms) arise at a high frequency during meiosis, which occurs during the mosquito phase of the life cycle. Further, recent studies on the PMMSA gene have revealed possible intragenic recombination events (11, 12). As this capacity for recombination could have implications for any future molecular vaccine, we have -analyzed the variation that occurs in P. falciparum chromosomes in further detail. We show here that there are indeed 14 chromosomes and assign a total of 25 markers to 12 of them in each of three different clones. The sizes of some chromosomes vary so much that their relative rates of migration...