The surface alignment of lyotropic chromonic liquid crystals (LCLCs) can be not only planar (tangential) but also homeotropic, with self-assembled aggregates perpendicular to the substrate, as demonstrated by mapping optical retardation and by three-dimensional imaging of the director field. With time, the homeotropic nematic undergoes a transition into a tangential state. The anchoring transition is discontinuous and can be described by a double-well anchoring potential with two minima corresponding to tangential and homeotropic orientation.PACS numbers: 42.70.Df Spatial bounding of a liquid crystal (LC) lifts degeneracy of molecular orientation specified by the director n and sets an "easy axis" n 0 at the surface. Deviation of n from n 0 requires some work thus establishing a phenomenon of "surface anchoring" that has been explored extensively for thermotropic LCs [1][2][3][4][5][6][7][8][9][10][11]. For lyotropic LCs, such as water solutions of polyelectrolytes, surfactants, dyes, etc., the studies of anchoring are scarce. The view is that the surface alignment of lyotropic LCs is determined by an excluded volume effect, which favors the longest dimension of building units to be parallel to a substrate [12][13][14][15]. We study surface phenomena in nematic lyotropic chromonic LCs (LCLCs), a distinct class of self-assembled LCs formed by water solutions of planklike molecules with polyaromatic cores and ionic peripheral groups [16]. Reversible chromonic assembly and mesomorphism are displayed broadly by dyes, drugs and nucleotides [16]. In water, the LCLC molecules stack face-to-face, forming elongated aggregates. The aggregates are not fixed by covalent bonds, being polydisperse with an average length l ∝ √ φ ln (E/k B T ) that depends on temperature T , volume fraction φ, and stacking energy E ∼ (4 − 10) k B T [17]. We demonstrate that in LCLCs, n 0 can be either parallel to a substrate (planar or tangential alignment, denoted "P") or perpendicular (homeotropic, or H alignment), with discontinuous transitions between the two, thus suggesting that both entropy and anisotropic molecular interactions control the surface phenomena.We study disodium cromoglycate (DSCG) [16], C 23 H 14 O 11 N a 2 (Spectrum Inc, purity 98%), dissolved in water at 15 wt % (mixture A) and 12.5wt% doped with 1.5wt% of Na 2 SO 4 (mixture B). The H alignment was achieved by treating glass plates with 1% water solution of N,N-dimethyl-N-octadecyl-3-aminopropyl trimethoxysilyl chloride (DMOAP) [2]. The two plates are separated by Mylar strips; the cell thickness d was measured by light interference technique. The cells were filled at T N I + 10 K, sealed with a UV-cured Norland epoxy glue, and cooled down to T = 298 K with a rate 5 K/ min in a thermal stage HS-1 (Instec, Inc.). We used an LC PolScope for in-plane mapping of opticale sin 2 θ −1/2 , θ is the angle between n and the normal z to the cell, n o and n e are the ordinary and extraordinary refractive indices, respectively. At 546 nm and T = 298 K, we determined n o = 1.37 ± ...