Determination of the number of parasite clones present in a malaria infection is usually based on Polymerase Chain Reaction (PCR) amplification of Plasmodium polymorphic genomic sequences from peripheral blood. This method however does not provide information on the developmental stages of the parasites detected, or on the potential trasmissibility of the detected genotypes to the Anopheles vector. Reverse Transcriptase-PCR assays on P. falciparum mRNAs produced specifically in sexual stages have been developed in the past few years in order to detect and genotype circulating gametocytes, the parasite transmission stages, and are discussed in this review. Assays based on P. falciparum gamete-specific gene pfs25 and gametocyte-specific polymorphic gene pfg377 can detect presence of subpatent gametocytes in infected blood, can identify the pfg377 allele(s) specifically carried by the sexual stages, and detect coexistance of gametocytes of different genotypes. These assay have been used for the first time in field studies in a region of Sudan where malaria is seasonal, and they characterised parasite clonality and pattern of gametocyte production in the subpatent parasitaemias observed in the long malaria-free season. The method of specifically detecting and genotyping gametocytes in natural infections is proving to be a useful tool in investigating parasite transmission dynamics in field studies. This approach can be further improved by developing a multilocus RT-PCR assay which includes additional polymorphic gametocyte-specific transcripts. Candidate genes can be identified from the available data on the P. falciparum genome sequence and from recent analyses of parasite stage-specific transcriptomes.