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The use of biodiesel requires the development of proper quantification procedures for biodiesel content in blends and in lubricants (fuel dilution in oil). Although the ester carbonyl stretch at 1746 wavenumbers (cm-1) is the most prominent band in the IR spectrum of biodiesel, it is difficult to use for quantification purposes due to a severe fluctuation of absorption strength from sample to sample, even at the same biodiesel content. We have demonstrated that the ester carbonyl fluctuation is not caused by variation in the ester alkyl chain length; but is most likely caused by the degree of hydrogen bonding of the ester functional group with water in the sample. Water molecules can form complexes with the ester compound affecting the strength of the ester carbonyl band. The impact of water on quantification of the biodiesel content of blends was significant, even for B100 samples that met the proposed ASTM D6751 water limit of 500 ppm by D6304 (Karl Fischer Methdod).