The screening for mutants and their subsequent molecular analysis has permitted the identification of a number of genes of Arabidopsis involved in the development and functions of the gynoecium. However, these processes remain far from completely understood. It is clear that in many cases, genetic redundancy and other factors can limit the efficiency of classical mutant screening. We have taken the alternative approach of a reverse genetic analysis of gene function in the Arabidopsis gynoecium. A high-throughput fluorescent differential display screen performed between two Arabidopsis floral homeotic mutants has permitted the identification of a number of genes that are specifically or preferentially expressed in the gynoecium. Here, we present the results of this screen and a detailed characterization of the expression profiles of the genes identified. Our expression analysis makes novel use of several Arabidopsis floral homeotic mutants to provide floral organ-specific gene expression profiles. The results of these studies permit the efficient targeting of effort into a functional analysis of gynoecium-expressed genes.The gynoecium is the fourth and innermost whorl of a typical bisexual flower. It is composed of the female reproductive organs, or carpels, and encloses the ovules, which develop into seeds after fertilization. The gynoecium may be composed of simple, unfused carpels, although in most species it is syncarpic, i.e. composed of several carpels fused together. The gynoecium functions to protect the ovules and to allow the operation of pollen-pistil incompatibility mechanisms. After fertilization, it develops into a fruit that participates in seed dissemination.In Arabidopsis, the gynoecium is a complex syncarpic structure. This first develops as an open-ended tube from a primordial dome in the center of the floral meristem. A vertical septum then forms internally from either side of the gynoecial tube, and the two halves of this septum fuse to divide the structure into two loculi. Placental tissues develop in the zones where the vertical septum and gynoecial wall meet to generate two rows of ovule primordia within each loculus. Each ovule consists of a seven-celled embryo sac of the Polygonum type (Fahn, 1975), together with a small nucellus and two covering integuments. Cell division occurring at the distal end of the gynoecial cylinder forms the style and stigma tissues. The stigma consists of a pappillate epidermal cell layer with a modified external wall and cuticle. This tissue receives and permits the germination of compatible pollen grains. After the penetration of the stigma by pollen tubes, a transmitting tissue in the style and vertical septum functions to guide the pollen tubes toward the ovules where fertilization takes place. After fertilization, the Arabidopsis gynoecium develops into a two-chambered, capsular fruit, termed a silique. This structure opens at maturity to release its seeds by rupture along four zones of dehiscence in the silique wall situated on either side of the vertic...