The three-dimensional (3-D) network of the granum-stroma thylakoid assembly of vascular plant chloroplasts exhibits complex structural/functional heterogeneity. A complete understanding of the ultrastructure of this assembly is critical for our understanding of thylakoid function. The prevailing historical model of thylakoid structure, based on information derived from serial section analyses of electron microscopy (EM) images, suggests a helical arrangement of stroma membranes wound around the granum stacks. More recently, electron tomography has emerged as the leading method for the study of thylakoid ultrastructure, as it provides for higher resolution in the depth dimension. The first detailed 3D topological model derived from electron tomography was in disagreement with the helical model, whereas a more recent electron tomography study, conducted under somewhat different experimental conditions, suggested that basic features of the helical model are still valid. Here, we review the conventional EM data and present a critical discussion of the two electron tomography data sets in an attempt to establish a consensus model that accommodates all the information presently available.