Predicting the 3D structures of molecules is a fundamental problem in both computational chemistry and biology (for small molecules and proteins respectively). In this talk, I'm going to introduce some of our recent work for molecular structure prediction with diffusion-based models including: (1) the first diffusion models for 3D molecular structure prediction, GeoDiff; (2) a diffusion model defined on Torsional space for protein side chain structure prediction, DiffPack, and a diffusion model for inferring multiple protein stable conformations, Str2Str.