During the last decade transcriptome analyses demonstrated that alternative splicing plays an important role to generate a large number of mRNA and protein isoforms from a limited number of genes. However, the frequency of the alternative splicing dramatically varies among living organisms. For example, 35-65% of human genes are involved in alternative splicing, whereas only a few are reported for unicellular organism yeast. Alternative splicing has been observed for several genes in the deadliest malaria parasite Plasmodium falciparum, but the frequency and the type were not systematically analyzed so far. In this study, we determined partial cDNA sequences for 88 open reading frames surrounding 246 introns in P. falciparum which were transcribed at schizont and gametocyte stages, and observed 15 instances of alternative splicing within a total of 14 gene transcripts, 16% of the analyzed genes. Among 5 basic splicing patterns, alternative 5' and 3' splicing, and intron retention were detected. Alternative splicing in 7 open reading frames had effects on the domain architectures of the gene products, which might result in modifying the cellular localization and function of these products.