The aim of the study was to compare quantitative and qualitative composition of β- fructooligosaccharides in onions: yellow (‘Oporto’), red (‘Karmen’), white (‘Alibaba’). Onions were analysed in October (hibernation) and March (activation). Mono-, di- and fructooligosaccharides (FOS) of DP 3-9 were determined in onions by HPLC method with the use of water-alcohol extracts. It was proved that the white onion was a good source of FOS (DP 6-9), which gave over 50% of total FOS (DP 3-9) in autumn only. At the same season the red onion was the richest in FOS (DP 3-5) and contained 5.3 g of FOS in 100 g of fresh weight, while the white onion contained 4.7 g in 100 g f.w. and yellow onion contained 2.7 g in 100 g f.w. Yellow onion had the best shelf life and contained stable amount of FOS (DP 3-5) ranging from 2.2 to 2.7 g/ 100 g. f.w. That amount covers only 25% of minimal requirement for prebiotic FOS needed for proper composition of bacterial flora in human colon.