Anthocyanins are a class of polyphenols responsible for the orange, red, purple and blue colors of many fruits, vegetables, grains, flowers and other plants. Consumption of anthocyanins has been linked as protective agents against many chronic diseases and possesses strong antioxidant properties leading to a variety of health benefits. In this review, we examine the advances in the chemical profiling of natural anthocyanins in plant and biological matrices using various chromatographic separations (HPLC and CE) coupled with different detection systems (UV, MS and NMR). An overview of anthocyanin chemistry, prevalence in plants, biosynthesis and metabolism, bioactivities and health properties, sample preparation and phytochemical investigations are discussed while the major focus examines the comparative advantages and disadvantages of each analytical technique.