The purpose of this study was to determine the changes in the contents of flavonoids that were the most prevalent in acacia and multifloral honey during one year of storage. Samples were stored in transparent glass containers, at room temperature, on open shelves exposed to light during daytime. Eight individual flavonoids identified and quantified using HPLC-Diode Array Detector (DAD) belongs to three subgroups: flavonols (quercetin, luteolin, kaempferol and galangin), total flavanons (hesperetin and pinocembrin) and total flavones (apigenin and chrysin). Obtained results revealed that multifloral honey had more total flavonoids than acacia samples did. On average from all of the samples, multifloral honey had more of quercetin, hesperetin, luteolin, kaempferol and apigenin than acacia honey did. Content of flavonoids increased in samples between the 1st and 6th month of storage and then started to decrease until the 9th month, when they remained relatively constant all the way until the 12th month of storage. In conclusion, acacia and multifloral honey after one-year of storage still can be a valuable source of flavonoids.