Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. New software for transmission electron tomography has been developed called TomoJ. TomoJ is a plug-in for the now standard image analysis & processing software for optical microscopy, ImageJ. TomoJ provides a user-friendly interface for alignment, reconstruction and a combination of multiple tomographic volumes & includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique & simultaneous iterative reconstruction technique), as well as the commonly used approach of weighted back-projection. The software presented is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.