Propolis has antibacterial, antiviral, antifungal, anti-inflammatory, antitumoral, antioxidant, immunomodulatory, tissue regeneration, anti-ulcer, analgesic, local anaesthetic, and antiseptic effects related to its chemical components. The aim of the present study was to determine certain biological active phenolic compounds and their levels in propolis collected from Bursa province, and to evaluate propolis quality and effects of altitude and season. Propolis samples were collected using propolis traps from 15 different constant apiaries at varying altitudes (between 50 and 1000 m) located in Bursa province Turkey, during the spring, summer and autumn of 2012. Fourteen flavonoid and phenolic acids in ethanolic extracts were investigated by liquid chromatography tandem-mass spectrometry (LC-MS/MS). Galangin, naringenin, pinocembrin, caffeic acid and caffeic acid phenylethyl ester were detected in all samples (45 samples) for all seasons and altitudes. Significant differences were determined for certain phenolic compounds levels across altitudes and seasons. In the present study results showed that qualitative and quantitative analysis of propolis for useful phenolic compounds may provide partial standardization of propolis depend on altitude and season.