Electron tomography provides opportunities to determine diree-dimensional cellular architecture at resolutions high enough to identify individual macromolecules such as proteins. Image analysis of such data poses a challenging problem due to the extremely low signal-to-noise ratios that makes individual volumes simply too noisy to allow reliable structural interpretation. This requires using averaging techniques to boost the signal-to-noise ratios, a common practice in electron microscopy single particle analysis where they have proven to be very powerful in elucidating high resolution structure. Although there are significant similarities in the way data is processed, several new problems arise in the tomography case that have to be properly dealt with. Such problems involve dealing with the missing wedge characteristic of limited angle tomography, the need for robust and efficient 3D alignment routines, and design of mediods that account for diverse conformations through the use of classification. We present a framework for reconstruction via alignment, classification and averaging of volumes obtained from limited angle electron tomography, providing a powerful tool for high resolution structure determination and description of conformational variability in a biological context. © 2007 IEEE.