Onion (Allium cepa L.) and garlic (Allium sativum L.), among the oldest cultivated plants, are used both as a food and for medicinal applications. In fact, these common food plants are a rich source of several phytonutrients recognized as important elements of the Mediterranean diet, but are also used in the treatment and prevention of a number of diseases, including cancer, coronary heart disease, obesity, hypercholesterolemia, diabetes type 2, hypertension, cataract and disturbances of the gastrointestinal tract (e.g. colic pain, flatulent colic and dyspepsia). These activities are related to the thiosulfinates, volatile sulfur compounds, which are also responsible for the pungent of these vegetables. Besides these low-molecular weight compounds, onion and garlic are characterized by more polar compounds of phenolic and steroidal origin, often glycosilated, showing interesting pharmacological properties. These latter compounds, compared to the more studied thiosulfinates, present the advantages to be not pungent and more stable to cooking. Recently, there has been an increasing scientific attention on such compounds. In this paper, the literature about the major volatile and non-volatile phytoconstituents of onion and garlic has been reviewed. Particular attention was given to the different methodology developed to perform chemical analysis, including separation and structural elucidation.