The Qohrud granitoid body of Miocene age is located 40 km SW Kashan, ranging in composition from granite through granodiorite to tonalite. Hydrothermal activities following the magma intrusion have brought about formation of various coarse automorphic and colored quartz crystals within the fractures and cavities of different lithologies. The quartz crystal varieties include transparent, semi-transparent, pale green, yellow and black crystals, as well as those with smoky and reddish brown roots and also crystals containing tiny acicular rutile inclusions. Mineral chemistry, as well as fluid and solid inclusion studies on the colored and automorphic quartz crystals indicate that various physical and chemical factors, such as temperature, pressure, magma and host rock compositions, hydrothermal fluids and the associated alterations, as well as pH and Eh were involved in the formation of these automorphic colored crystals. The solid inclusions within these automorphic quartz crystals might have formed in two ways: 1) introduction of the necessary elements for the formation of quartz and the solid inclusions by the fluids and then, entrapment of these inclusions within the growth layers of quartz crystals; 2) direct introduction of very fine mineral particles within the growth layers of quartz, leading to occurrence of various colored crystals. Smoky crystals can be formed by the replacement of Si by Al and also by the presence of U and Th within them. The reddish color of quartz crystals was recognized as the result of the presence of fine rutile needles. Automorphic black-colored quartz crystals are formed at oxidant and almost high pH conditions by initial precipitation of magnetite and then, manganese oxides at the outermost growth layers. The green quartz crystals have been resulted from chloritic and epidotic alterations within the host and neighboring rocks.