For the further optimization of antibody expression in plants, it is essential to determine the final accumulation sites of plant-made antibodies. Previously, we have shown that, upon secretion, IgG antibodies and Fab fragments can be detected in the intercellular spaces of leaf mesophyll cells of transgenic Arabidopsis thaliana plants. However, immunofluorescence microscopy showed that this is probably not their final accumulation site. In leaves, IgG and Fab fragments accumulate also at the interior side of the epidermal cell layers and in xylem vessels. These accumulation sites correspond with the leaf regions where water of the transpiration stream is entering a space impermeable to the proteins or where water is evaporating. In roots, plant-made Fab fragments accumulate in intercellular spaces of cortex cells, in the cytoplasm of pericycle and, to a lesser extent, endodermis cells, and in cells of the vascular cylinder. In other words, antibody accumulation occurs at the sites where water passes on its radial pathway towards and within the vascular bundle. Taken together, our results suggest that, upon secretion of plant-made antibodies or Fab fragments, a large proportion of these proteins are transported in the apoplast of A. thaliana, possibly by the water flow in the transpiration stream.