Chia is a food plant producing seeds which have seen increasing interest owing to their health benefits. This work is the first report on the metabolite profile, total polyphenols and antioxidant activity of chia seeds, determined by ultrasound-assisted extraction, coupled with gas chromatography-mass spectrometry (UAE GC-MS). Different chia sources were compared: two commercial (black and white) and three early flowering (G3, G8 and G17) mutant genotypes. Organic extracts were mainly composed of mono- and polyunsaturated fatty acids with alpha-linolenic being the most abundant. Polar extracts contained sucrose, methylgalactoside and glucose as main sugars. Antioxidant activity and total polyphenolic content were correlated. Chemical composition and yield potential of early flowering genotypes were different from commercial chia, and while white chia showed the highest content of omega-3 fatty acids, the high content of nutraceuticals in G17 and G8 suggests them as a potential source of raw materials for the food/feed industry.