Kava is a non-alcoholic beverage prepared by cold water extraction of the ground roots and stumps of Piper methysticum Forst. f. Kava contains flavokawains (FKs) which have been suspected of being potentially cytotoxic. Current HPLC protocols are not adapted to high-throughput quantification before export. The objectives of the present study were (i) to analyse with HPTLC the individual FKs in roots, stump, stems and peelings of four varieties grown in a controlled environment; (ii) to quantify FKs in 1053 commercial samples exported from Vanuatu in 2017-18-19 (370 roots, 381 chips and 302 powders) and (iii) to assess the efficiency of a colorimetric test for routine control. HPTLC plate scanning at 355 nm offered good linearity for three FKs with R2 > 0.99 and RSD < 3.0%. High total FKs (> 14 mg/g DW) were found in poor-quality varieties and in peelings unsuitable for consumption. Plant parts known for their good quality, such as roots and peeled stumps of noble varieties, presented low total FKs (< 7 mg/g). Great variation was observed in exported roots (2.53–24.56 mg/g), chips (2.73–18.03 mg/g) and powders (2.92–16.41 mg/g). HPTLC proved reproducible for the high-throughput quantification of FKs in kava. A positive relationship was confirmed between the absorbance of the acetonic extract and the total FKs (R2= 0.5211) (n = 1053). Multivariate analyses revealed that in roots, chips and powders, the three FKs are significantly correlated with high absorbance values. The absorbance of the acetonic extract gives a fair assessment of the FK content in kava products.