This review addresses recent advances in the analysis of organic contaminants, such as antibiotics, pesticides, biological toxins, and food-borne pathogens, in foods by capillary electrophoresis (CE). Special attention is paid to those aspects that increase sensitivity and/or selectivity, such as sample extraction and concentration, on-line preconcentration techniques (stacking), affinity capillaries or/and specific detectors (laser induced fluorescence (LIF), mass spectrometry (MS)). The various CE modes used to separate the compounds and the quantification strategies are also examined. As a result, this work presents an updated overview on the principal applications of CE, together with a discussion of their main advantages and drawbacks, and an outline of future trends in the analysis of organic contaminants in food.