Coffee has been one of the most commercialized food products and most widely researched beverage in the world for decades. It is considered a functional food, primarily due to its high content of compounds that exert antioxidant and other beneficial biological properties. This review summarized the data from analysis of coffee components, both volatile constituents and non-volatile high-molecular weight compounds performed by various chromatographic methods. A list of compounds identified by gas chromatography with mass spectrometry which define the aroma of coffee is provided. Publications on the measurement of methylxanthines (caffeine, theobromine, and theophylline), chlorogenic acids, diterpenes, sugars, amino acids, gamma-aminobutyric acid, dibasic acids, anions, and other compounds by HPLC and UHPLC-MS are reviewed. An overview of publications on the determination of organic contamination in coffee (PAHs, acrylamides, mycotoxins, etc.) and ways to reduce contamination through production technology and brewing methods are presented. Finally, an overview of the literature on authentication assessment for different grades of coffee grown in different regions is provided.