Homeodomain proteins are key regulators of patterning during the development of animal and plant body plans. Knotted1-like TALE homeodomain proteins have been found to play important roles in the development of the Arabidopsis shoot apical meristem and are part of a complex regulatory network of protein interactions. We have investigated the possible role of the knotted1-like genes KNAT1, KNAT3, KNAT4, and KNAT5 in Arabidopsis root development. Root growth is indeterminate, and the organ shows distinct zones of cell proliferation, elongation and differentiation along its longitudinal axis. Here we show that KNAT1, KNAT3, KNAT4 and KNAT5 show cell type specific expression patterns in the Arabidopsis root. Moreover, they are expressed in different spatially restricted patterns along the longitudinal root axis and in lateral root primordia. Hormones play an important role in maintenance of root growth, and we have studied their effect on KNAT gene expression. We show that KNAT3 expression is repressed by moderate levels of cytokinin. In addition, we show that the subcellular localization of KNAT3 and KNAT4 is regulated, indicating post-translational control of the activities of these transcription factors. The regulated expression of KNAT1, KNAT3, KNAT4 and KNAT5 within the Arabidopsis root suggests a role for these genes in root development. Our data provide the first systematic survey of KNAT gene expression in the Arabidopsis root.