Abstract: Transition state (TS) search is key in chemistry for elucidating reaction mechanisms and exploring reaction networks. The search for accurate 3D TS structures, however, requires numerous com- putationally intensive quantum chemistry calculations due to the complexity of potential energy surfaces. Here, we developed an object-aware SE(3) equivariant diffusion model that satisfies all physical symmetries and constraints for generating sets of structures – reactant, TS, and product – in an elementary reaction. Provided reactant and product, this model generates a TS structure in seconds instead of hours, which is typically required when performing quantum chemistry-based optimizations. The generated TS structures achieve a median of 0.08 Å root mean square deviation compared to the true TS. With a confidence scoring model for uncertainty quantification, we approach an accuracy required for reaction barrier estimation (2.6 kcal/mol) by only performing quantum chemistry-based optimizations on 14% of the most challenging reactions. We envision the proposed approach useful in constructing large reaction networks with unknown mechanisms.