Study of the expression patterns of the genes encoding granule-bound starch synthase (GBSS) and branching enzyme (BE) in in vitro cultured cassava ( Manihot esculenta Crantz) plants revealed that they are organ-specifically and differentially expressed; GBSS is more abundantly expressed in leaf than in stem, while the reverse is true for BE. Furthermore, it was found that in almost all organs of in vitro grown plants, GBSS and BE are much more expressed than in the corresponding organs of greenhouse grown plants. Transcript levels of both genes are strongly induced by the exogenous supply of metabolizable carbohydrates such as sucrose, glucose and fructose. For sucrose induction, an optimum concentration could be established which differed for the two genes. Tuberous roots could not be obtained from in vitro grown cassava plants, which instead formed thickened stems. These thickened parts of the stem contained large amounts of starch but did not contain more transcript of either GBSS or BE than normla parts of the stem. The possible use of thickened stem starch for screening a large number of transgenic cassava plants in an in vitro system is discussed.