Seeds of oil flax (Linum usitatissimum) are rich in polyunsaturated fatty acids and their composition is one of the major criteria for flax selection. Conventional breeding schemes take many years and need a lot of space in greenhouses and/or in fields to achieve genotypes with the desired traits. We have improved the half-seed method that allows flax line selection from their oil seed composition. Cotyledon tips were analysed by GC to determine their FAME profiles while the remaining seed was sown to regenerate flax plant. An optimisation of the GC enabled a sample to be analysed every 4 minutes. Such a technique could be applied without loss of germination rate for excised seeds. Further experiments showed that both seed parts had the same fatty acid profile as cotyledon tips. This non-destructive procedure based on the half-seed method and ultrafast GC analysis provides an efficient screening of flax genotypes according to their seed fatty acid composition over only one generation.