Bioactivity-guided fractionation of Polygala alpestris L. (Rchb.) extracts led to the identification of two new xanthones, 1,3,7-trihydroxy-2,6-dimethoxyxanthone (1) and 2,3-methylenedioxy-4,7-dihydroxyxanthone (2). In addition five known compounds 3,4-dimethoxy-1,7-dihydroxyxanthone (3), 1,3-dihydroxy-7-methoxyxanthone (4), 1,7-dihydroxy-2,3-dimethoxyxanthone (5), 3′,6-O-disinapoyl sucrose (6) and 3′,5′-dimethoxybiphenyl-4-olo (7) were isolated. The structures of the isolated compounds were established by means of high resolution mass spectrometry, mono- and bi-dimensional NMR spectroscopy. All isolated compounds were tested for cytotoxic activity against three tumor cell lines (LoVo, HL-60, K 562).