We have controlled the spatial distribution of organic nanocrystals grown in sol-gel thin films prepared by spin-coating. This spatial control of nucleation is carried out through the difference in confinement between the surface and the depth of the sol-gel thin films at the first stage of the coating process. Thus, we can direct the nucleation sites in grooves or wells of textured substrates. We have achieved, respectively 1- and 2-D ordering of nanocrystals while 3-D patterns have been obtained through a multi-layer process. This nucleation control gives an opportunity to design new 3-D optical data storage or 2-D arrays of luminescent crystals for chemical or biological multi-sensors. (c) 2005 Elsevier B.V. All rights reserved.