This paper presents a method for the fabrication of integrated porous silica layers in microfluidic channel networks by microfabrication techniques. Porous silica is obtained by anodization of silicon, followed by full conversion of the porous silicon network into porous silica by means of thermal oxidation. A series of experiments were performed with various channel layouts to determine the critical parameters, including the I–V characteristics and the optimal working potential for stable pore formation, during anodic etching. Typical test structures were anodized in 5% HF for 15 min at 1 V, yielding an average pore size of around 5.4 nm and porosity of 49%. Complete conversion of porous silicon into porous glass was accomplished with wet oxidation at 900 °C. The average pore size and porosity of porous glass network were around 3.8 nm and 34%, respectively. This decrease in both pore size and porosity is caused by the increase in molar volume when silicon oxidizes to silicon oxide. The transparency and the hydrophilicity of porous glass layers are evidenced by means of monitoring the diffusion of Rhodamine B fluorescent dye through the porous network. This fabrication method can be applied to (3-D) structured microfluidic channels and it is envisioned that the resulting porous silica layers can be employed for a wide range of application areas, such as membrane technology, catalyst supports, chromatography and electrokinetics.