Spinodal decomposition in siloxane sol-gel systems has been investigated in a macroporous silica mould (pore diameter D = 2.74 µm) with a bicontinuous structure. Methyltrimethoxysilane (MTMS) and tetramethoxysilane (TMOS) have been employed as siloxane gel sources and as-sintered hydrophilic and octadecylsilylated hydrophobic macroporous silica were used as the confining moulds. In an MTMS-formamide system with a longer phase separation time and higher viscosity, the phase-separated gels in both moulds exhibited a similar morphology when the bulk correlation length Λ, i.e. spinodal wavelength in a free volume, was enough shorter than D. As Λ was made longer by altering the starting composition, a wetting transition occurred in both the hydrophilic and hydrophobic moulds. In an MTMS-methanol system with a shorter phase separation time and lower viscosity, the wetting transition unexpectedly occurred when Λ was much shorter than D in the hydrophobic mould. In TMOS-formamide system, fine and disordered structure has formed in the hydrophilic mould and never exhibited the wetting transition. A hydrodynamic wetting transition in each system was considered to occur when the ratio D/Λ becomes smaller than unity, whereas a diffusive wetting transition takes place in the early stage of spinodal decomposition in the case where the chemical affinity between siloxane gel and the mould is high. Additionally, when the initial wavelength of spinodal decomposition is shorter than D, spinodal decomposition is highly suppressed due to the presence of the random surfaces of macropores. These effects may interplay depending on the physical and chemical nature of the sol-gel systems and the moulds.