In this study, 266 cDNA clones were isolated from a cDNA library made from mRNA of three-week-old root nodules of Lotus japonicus, employing a degenerate oligonucleotide probe that corresponds to a conserved region of small GTP-binding (SMG) proteins. The clones were sorted into groups by cross hybridization and 3' sequencing, and 33 contigs were sequenced in an orderly fashion. Twenty-seven complete and six incomplete protein structures were deduced, which represent three subfamilies of the superfamily of signal transducing GTP-binding proteins. The 33 proteins are divided into nine subclasses, of which seven belong to the Ypt/Rab subfamily, one subclass represents the Rho/Rac subfamily, and one subclass represents the Ran subfamily of small GTP-binding proteins. The protein sequences were compared with related proteins from other plants, from mammals and other species, and discussed with respect to structure and function in different cellular processes. It is apparent that the number of genes encoding SMG proteins in plants must be quite large, since the large number of subclasses found in other eukaryotes is not fully represented in our analysis. Transcription patterns through root nodule development were analysed for 27 of the 33 cDNAs. Differential expression patterns may reflect whether the coded gene product is of importance for organ development. Most mRNAs appear to be constitutively expressed; however, a few unique mRNAs representing the subclasses Rab1, Rab2, Rab5, Rab7 and Rac show elevated levels in root nodules, and certain Rab7, Rab8 and Rab11 species are enriched in aerial parts of the plant. This suggests that most small GTPases have household functions, whereas a few may be required for specialized activities that are important for specialized cells.