3MOTIF is a web application that visually maps conserved sequence motifs onto three-dimensional protein structures in the Protein Data Bank (PDB, Berman et al., Nucleic Acids Res., 28, 235-242, 2000). Important properties of motifs such as conservation strength and solvent accessible surface area at each position are visually represented on the structure using a variety of color shading schemes. Users can manipulate the displayed motifs using the freely available Chime plugin.