Selected alkaloids are chromatographed on cyanopropyl-silica thin layers using various nonaqueous and aqueous eluents. Because of the strong retention of these basic compounds, nonaqueous eluents containing medium polar diluents, strongly polar modifiers, and silanol blockers (ammonia or diethylamine) are required for separation. Likewise, aqueous eluents containing modifiers (acetonitrile, methanol, and tetrahydrofuran), buffered aqueous solutions at pH 2-8, ion-pair reagents [octane sulfonic acid sodium salt, sodium dodecyl sulphate, and bis-(2-ethylhexyl)phosphoric acid], or silanol blockers (ammonia, tetrabutyl ammonium chloride, and diethyl amine) are investigated. The separation selectivity as well as spot symmetry and efficiency system in the applied eluent systems are analyzed. The most selective and efficient systems are used in two-dimensional separations of isoquinoline alkaloids' mixture and the plant extracts Chelidonium majus, Fumaria officinalis, and Glaucium flavum. Two-dimensional thin-layer chromatography on cyanopropyl layer with diode array detection densitometry enables the separation and identification of some alkaloids in plant extracts.