Agapanthus (Agapanthus praecox ssp. orientalis), a liliaceous perennial, is cultivated as an ornamental plant because of its beautiful, blue-violet to white flowers. We have previously produced transgenic plants containing the ß-glucuronidase (GUS) reporter gene under the control of cauliflower mosaic virus (CaMV) 35S promoter in an experimental strain of Agapanthus via Agrobacterium-mediated genetic transformation. These transgenic plants have been cultivated for 5 yr after transplantation to pots. In the present study, we carried out morphological characterization, and examination of the ploidy level, pollen fertility and stability of GUS gene expression in 12 transgenic plants derived from five independent lines at the flowering stage. Flow cytometry (FCM) analysis indicated that transgenic plants of four lines kept the diploid level, but those of the remaining one line were tetraploid. For all of the 12 transgenic plants, some morphological variations were observed both in vegetative and floral organs such as decreased number of leaves per inflorescence, smaller leaves, shorter inflorescence stalks, decreased number of florets per inflorescence and smaller florets. Pollen fertility of all the transgenic plants was below 5% as determined by acetocarmine staining. All the 12 transgenic plants showed stable expression of the GUS gene in leaves, roots, tepals, pistils, and stamens, as indicated by histochemical GUS assay, fluorometric GUS assay, and/or real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis. No apparent GUS gene silencing was observed in transgenic agapanthus plants even after 5 yr of cultivation.