mTM-align is a server for efficient protein structure comparisons, which includes are two related modules. The first is for fast database search with one input structure. The second is for multiple structure alignment with two or more input structures. For the first module, it takes about 2-5 minutes for a structure of a medium size (~300 residues). After the search is done, a multiple structure alignment is performed automatically with the top 10 structure, using the second module. The users are also able to select other structures from the returned list to perform multiple structure alignment. For the second module, it takes a few seconds for input of ~10 structures of medium size.