The physical properties, total phenols, total flavonoid content and free radical scavenging activities of honey samples from Malaysia were investigated. The physical properties of Tualang, Gelam and Acacia honey samples, in terms of pH, color, moisture, electrical conductivity and total soluble solid were significantly different (p = 0.000). Gelam honey was reported to have the highest total phenols (606.17 mg GAE/kg honey) and flavonoid content (183.43 mg RE/kg honey). Tualang honey was reported to have the highest free radical scavenging activity with the IC50, 72.75 g/L compared to Gelam (77.41 g/L) and Acacia (90.83 g/L). There is no significant difference has been revealed among honey samples for radical scavenging activity (p = 0.827). Nevertheless, strong correlation was obtained between pH, color, electrical conductivity and total soluble solid with the scavenging activity of all honey samples with the correlative coefficient, r = 0.979, 0.902, 0.917 and 0.957, respectively. The establishment of the statistical correlation could be useful for honey related industry.