Granite countertops are unusual among counter materials used today. While most other counters, including those made of quartz, are produced in a factory, granite is produced in the earth, which means that no two granite counters will ever look exactly the same twice as the mix of minerals, heat and pressure that created them can never be duplicated. Some of granite's natural characteristics can be viewed as flaws by the consumer. Understanding what these are may help you to view your granite's markings not as flaws but as character.
One flaw frequently pointed out by consumers of granite counters is the colour of the counter. Because granite gets its colouration from minerals in the earth where it was formed, there may be large patches or areas of colour that do not appear to be part of the rest of the counter, which may mean large black spots that appear to be stains or distinct colour changes from one end to the next, such as in stones like Verde Fuoco, which can vary from red to green from one end to the next. These are not defects of the stone but are merely the natural variation present in all granite, taken to an extreme in some stones.
Fissures are small, thin "cracks" in the granite that formed when the stone did. Most often they are not structural, meaning they will not affect the strength or use of the granite. They may widen slightly over time, particularly if exposed repeatedly to hot objects such as pots fresh from the stove. Fissures are not considered a defect or flaw by the stone industry. Many stones contain them on the back or underside of the stone but were polished away on the surface. Other stones have small surface fissures that are not readily apparent due to the light reflecting off the polished stone around the fissure. If a fissure is present in the slab you are purchasing, request that this section be used as a cutout, if possible, if its presence bothers you. If a fissure widens after installation, fill it with a granite repair kit to minimise its appearance.
Like fissures, small surface pits may have formed in the stone while it was created. Some stones are more prone to pits than others; stones with a high mica content like Labrador Antique will have numerous small pits across the surface. These pits are too small to be felt and are easily disguised by polishing the stone; light bouncing off the surface will obscure them from view. Honing the stone will make them more apparent. Pits do not affect the structure of the stone and are not considered defects or flaws by the fabricator. They do not typically widen or increase in size over time.
Occasionally, large pieces of clear quartz appear in a slab of granite. The quartz will give the granite slab the appearance that it is transparent; you can sometimes see deep into the stone through a quartz section. Surrounding the quartz may be large sections of fissures and pits that fracture out of the quartz. The quartz section itself may also contain large fissures or fractures inside it, while the top is smooth to the touch. These quartz pits are not considered defects or flaws and are highly sought out in some cases for the interest they bring to the stone.