Abstract-Lyotropic chromonic liquid crystals (LCLC) are a kind ofLCs far less known and more difficult to control than conventional thermotropic nematics. Nevertheless, LCLCs are a preferred optionoften the only one-for applications where hydrophilic materials must be employed. Being water-soluble, LCLC can be used in numerous biology related devices, for example in target detection in lab-on-chip devices. However, their properties and procedures to align them are still less explored, with only a very limited number of options available, especially for homeotropic alignment. In this work, novel organic alignment layers and alignment properties have been explored for selected LCLCs. Non-conventional organic alignment layers were tested and new suitable procedures and materials for both homogeneous and homeotropic alignments have been found.Lyotropic chromonic liquid crystals (LCLC) are not as ubiquitous as their thermotropic nematic liquid crystal counterparts. However, their hydrophilic character make them perfect candidates for a number of specific applications, particularly those where biological materials are involved. In this context, LCLCs are being recognized as a simple and inexpensive method for detection of biologically active macromolecules or microorganisms [1][2][3] as well as a standard procedure for microparticle detection in hydrophilic media.LCLCs are well suited for these applications, providing aligning surfaces compatible to aqueous media are employed. Organic alignment layers, such as polyimides and polyamides are well-known layers for conventional thermotropic liquid crystals. However, they are not commonly employed as alignment layers for lyotropic liquid crystals. LCLC can be aligned onto organic surfaces such as certain polymers, [4,5] graphene, parylene films, (PMMA) films, fluoropolymer films [6] or other techniques, such as micropatterned substrates [7]. The alignment of LCLC on inorganic surfaces such as SiO 2 and SiOx has been demonstrated elsewhere [8] In this work, a study of novel alignment layers for water-based lyotropic liquid crystals has been carried out, testing new non-conventional layers, seldom utilized for thermotropic liquid crystal alignment. Some of the new tested compounds produced well aligned LCLC layers * E-mail: eva.oton@nikon.com and two new layers were found to align the LCLC in homeotropic configuration.Some of these layers are suitable to eventually work as a starting point for surface functionalization protocols in biological applications.The lyotropic chromonic liquid crystals chosen were Sunset Yellow FCF (disodium 6-hydroxy-5-[(4-sulphonatophenyl)azo]naphthalene-2-sulphonate) and Cromolyn (sodium cromoglicate, a well-known traditional treatment for asthma), both being watersoluble salts of organic acids. Despite Cromolyn being more studied, Sunset Yellow (SSY) was preferred, because SSY presents a wider range of concentration where the nematic phase appears: 27% < N < 35% w/w at RT, (compared to Cromolyn: 13% < N < 17% w/w at RT) [9], as well as a wider t...