Kava (Piper methysticum) is used to prepare the traditional beverage of the Pacific islands. In Europe, kava has been suspected to cause hepatoxicity with flavokavin B (FKB) considered as a possible factor. The present study describes an HPTLC protocol for rapid screening of samples. The objectives are: to detect the presence of flavokavins in extracts and to compare the FKB levels in different cultivars. Overall, 172 samples originating from four cultivars groups (noble, medicinal, two-days and wichmannii), were analysed. Results indicate that the ratio FKB/kavalactones is much higher in two-days (0.39) and wichmannii (0.32) compared to nobles (0.09) and medicinal cultivars (0.10). For each group, the ratios flavokavins/kavalactones do not change significantly between roots, stumps or basal stems and among clones, indicating that they are genetically controlled. This protocol has good accuracy and is cost efficient for routine analysis. We discuss how it could be used for quality control.