When the spirit is distilled it is completely colourless. The colour of the whisky when you see it in the bottle (and the glass) is a result of the maturation process. To be classified as a whisky, the spirit must have spent at least 3 years in Oak barrels, and fulfil varying other requirements depending on sub-category (Scotch, Bourbon, Tennessee, Rye, etc.). The colour comes from these Oak Barrels, and the intensity of the colour in the whisky is dependent on the prior usages of the barrels. Due to the intensity of fresh oak, Scotch whisky distillers use oak barrels which have previously been used to mature other drinks, predominantely either Bourbon or Sherry, as these drinks can take out much of the harsh richness of the oak which would otherwise overpower the delicate flavours of the whisky. Whisky matured in "First Fill" sherry barrels extract the deepest, richest, darkest colour from the oak accompanied by lots of sweet, fruity tannins. When this first fill has been removed from the barrel after 10years or so and bottled for sale, the barrel may be reused for maturing more whiskies. This is then called "Refill" or "Second (/Third) Fill" and the whiskies that are matured in these barrels will extract less rich colours and flavours through their respective usages. Whisky matured in first fill Bourbon barrels however, naturally draw less colour from the oak, generally resulting in a yellowish, straw-like colour; while the flavours extracted are likely to be more vanillin, citrusy, and floral spices. The reason for the difference in colour extraction between Sherry and Bourbon barrels is in the way that the sherry and bourbon themselves were matured. Sherry matures in an open cask to encourage oxidation, whereas whiskies mature in closed casks to avoid unwanted air contact. It is exactly this oxidation which turns sherry into it's dark colour, and which permeates into, and settles in the oak - which is in turn extracted by the maturing "whisky" spirit.