We present a study of the structure and evolution of the high-redshift intergalactic medium (IGM) using a variety of approaches based on high-resolution quasar spectra. We first use the cross-correlation of transmitted flux towards two pairs of quasars with moderate angular separation to demonstrate that filamentary structures in the IGM at z = 4 are partially coherent on roughly 1 Mpc scales. We then measure the ionization state of the high-redshift IGM using three techniques: a search for low-ionization metal lines at z > 5, an analysis of the evolution of Lyman-alpha optical depths over 2 2.