The principle, characteristics and applications of molecular imaging with terahertz electromagnetic waves are reviewed herein. The terahertz molecular imaging (TMI) technique uses nanoparticle probes to achieve dramatically enhanced sensitivity compared with that of conventional terahertz imaging. Surface plasmons, induced around the nanoparticles, raise the temperature of water in biological cells, and the temperature-dependent changes in the optical properties of water, which are large in the terahertz range, are measured differentially by terahertz waves. TMI has been applied to cancer diagnosis and nanoparticle drug delivery imaging. The technique is also compared with magnetic resonance imaging by using a dual-modality nanoparticle probe.