Seeds of Brassica napus (oilseed rape, canola) accumulate large amounts of phenolic compounds, mainly sinapine and various other sinapate esters. Sinapate esters are considered as anti-nutritional factors and prevent the use of the protein rich seed meal as food and feed. Within the scope of this work the comprehensive characterization of qualitative and quantitative alterations of the metabolic profile of selected transgenic oilseed rape with low sinapate ester content was performed. The seed-specific suppression of UGT84A9 (UDP-glucose:sinapate glucosyltransferase) led to a reduction of the total sinapate ester content to 44 %. The co-suppression of UGT84A9 and BnSCT (1-O-sinapoylglucose:choline sinapoyltransferase) resulted only in a reduction to 63 % relative to the untransformed control. The most effective strategy was the seed-specific suppression of UGT84A9 combined with the overexpression of a sinapine esterase (BnSCE3) that decreased the sinapate ester content to 6 – 8 %. The analysis of the metabolite profile during seed and seedling development confirmed the seed-specific suppression of sinapate ester biosynthesis. The metabolite profiling revealed drastic and sophisticated changes of the seed metabolome, especially for mature dry seeds. These changes allow first hypotheses about the altered metabolite flux through the phenylpropanoid pathway. The fitness of the plants was not affected under greenhouse conditions. Seedlings showed a delayed accumulation of sinapoylmalate, which, however, did not interfere with the UV-B stress response. Agronomic traits such as oil content or protein content were not altered.