Tsetse flies (Diptera: Glossinidae) harbour three different symbiotic organisms in addition to the pathogenic African trypanosomes they transmit. The two gut-associated symbionts (primary, P; secondary, S) are enteric and are nutritionally required, whereas the third microorganism Wolbachia (family Rickettsiaceae) affects the reproductive biology of the insects it infects. The bacteriome-associated P-symbiont (Wigglesworthia glossinidia) displays a concordant phylogeny with its host tsetse species, whereas midgut S-symbionts characterized from distant tsetse have identical 16S rDNA sequences and therefore may either represent recent independent acquisitions or horizontal transfer between species. The S-symbionts have been cultured in vitro and a genetic transformation system has been developed. Here we report on their density and tissue tropism in different species (G. m. morsitans, G. p. palpalis, G. austeni and G. brevipalpis) and on their maternal route of transmission to tsetse progeny. Using a bacterium-specific PCR-assay, the S-symbionts were found primarily in the midgut, haemolymph, milk gland and in G. palpalis also in salivary glands of teneral flies. In older flies these infections were found to spread to other tissues including muscle, testes and fat body. The S-symbionts were transformed to express the marker gene product, Green Fluorescent Protein (GFP) in vitro. When the recombinant symbionts were introduced into the haemoceal of fertile female flies via intrathoracic microinjection, they were detected in the intrauterine progeny, indicating that haemolymph may provide a possible route for their transmission. The implications of these results for symbiont-host interactions and for transgenic strategies in tsetse are discussed.