Honey and propolis are rich in phenolic compounds, which act as natural antioxidants, and are becoming increasingly popular because of their potential role in contributing to human health. These compounds can also be used as indicators in studies into the floral and geographical origin of the honey and propolis themselves. We present here an overview of current analytical methods for measuring polyphenols in honey and propolis. The analytical procedure to determine individual phenolic compounds involves their extraction from the sample, analytical separation and quantification. The techniques reviewed are based on spectrophotometry as well as analytical separation techniques such as gas chromatography, high-pressure liquid chromatography and capillary electrophoresis.