Samples of Thymus alsarensis Ronniger, an endemic species for the Allchar locality, were evaluated for their polyphenolic composition and heavy metals. Allchar district is an abandoned antimony-arsenic-thallium deposit in the north-west of Kožuf Mountain, R. Macedonia, with a unique mineral composition affecting the mineral composition of the flora. A systematic method for phenolic compounds characterization was developed using mass spectrometry coupled to HPLC/DAD. Analyses were focused on the polyphenolic compounds to establish a possible correlation to the region specific heavy metals As and TI in the different organs of T. alsarensis. Twenty-seven polyphenols: phenolic acid derivatives and flavonoid glycosides of luteolin, apigenin, quercetin, and kaempferol were detected; contents were higher in the leaves and flowers compared with stems and roots. Quinic acid (1), prolithospermic acid (6), salvianolic acid B (7), salvianolic acid A (8), monomethyl lithospermate (9), luteolin dihexoside (12), luteolin pentosyl-hexoside (14), luteolin acetyl pentosyl-hexoside (16), luteolin acetyl hexoside (17), luteolin dipentoside (21), luteolin pentoside (24), luteolin acetyl dipentoside (25), kaempferol pentosyl-hexoside (19) and kaempferol acetyl pentosyl-hexoside (22) were detected in T. alsarensis for the first time. To assay the content of As and TI, root, stem, leaf and flower samples were analyzed by inductively coupled plasma atomic emission spectrometry (ICP-AES). Significant accumulation of As and TI was observed with As content from 0.25 to 140 mg/kg and TI from 0.10 to 496 mg/kg. The content of As was much higher in the roots, while the content of TI was significantly higher in the roots, flowers and leaves in all T. alsarensis specimens. Comparison of the results obtained for total polyphenols and for As and TI content does not suggest any correlation (positive or negative) between the total phenolic content and the content of TI and As. On the other hand, it is evident that the soil rich with specific heavy metals (TI and As) affects the type of polyphenolic compounds produced in different organs, compared with other Thymus species growing on soil that is not contaminated.