A comparison study of different extraction and clean-up procedures for the liquid chromatographic analysis of fumonisins B(1) (FB(1)) and B(2) (FB(2)) in corn masa flour was performed. The procedures included extraction (heat or room temperature) with acidic conditions or EDTA-containing solvents, and clean-up by immunoaffinity or C18 solid-phase extraction columns. Thereafter an analytical method was optimised using extraction with an acidic mixture of methanol-acetonitrile-citrate/phosphate buffer, clean-up through the immunoaffinity column and determination of fumonisins by liquid chromatography with automated pre-column derivatisation with o-phthaldialdehyde reagent. Recovery experiments performed on yellow, white and blue masa flours at spiking levels of 400, 800 and 1200 µg kg(-1) FB(1) and of 100, 200 and 300 µg kg(-1) FB(2) gave overall mean recoveries of 99% (±6%) for FB(1) and 88% (±6%) for FB(2). Good recoveries (higher than 90% for both FB(1) and FB(2)) were also obtained with corn tortilla chips. The limits of quantification of the method (signal-to-noise ratio of 10) were 25 µg kg(-1) for FB(1) and 17 µg kg(-1) for FB(2). The method was tested on different commercial corn masa flours as well as on white and yellow corn tortilla chips, showing fumonisin contamination levels (FB(1) + FB(2)) up to 1800 µg kg(-1) (FB(1) + FB(2)) in masa flour and 960 µg kg(-1) in tortilla chips. Over 30% of masa flours originating from Mexico exceeded the European Union maximum permitted level.