Plant family 1 UDP-dependent glycosyltransferases (UGTs) catalyze the glycosylation of a plethora of bioactive natural products. In Arabidopsis thaliana, 120 UGT encoding genes have been identified. The crystal-based 3D structures of four plant UGTs have recently been published. Despite low sequence conservation, the UGTs show a highly conserved secondary and tertiary structure. The sugar acceptor and sugar donor substrates of UGTs are accommodated in the cleft formed between the N- and C-terminal domains. Several regions of the primary sequence contribute to the formation of the substrate binding pocket including structurally conserved domains as well as loop regions differing both with respect to their amino acid sequence and sequence length. In this review we provide a detailed analysis of the available plant UGT crystal structures to reveal structural features determining substrate specificity. The high 3D structural conservation of the plant UGTs render homology modeling an attractive tool for structure elucidation. The accuracy and utility of UGT structures obtained by homology modeling are discussed and quantitative assessments of model quality are performed by modeling of a plant UGT for which the 3D crystal structure is known. We conclude that homology modeling offers a high degree of accuracy. Shortcomings in homology modeling are also apparent with modeling of loop regions remaining as a particularly difficult task.