The isotopically labeled compounds [5,6-(2)H(2)]-(Z)-1, 5-octadien-3-one (d-I) and [1-(2)H(1;2),2-(2)H(1;1)]-1-octen-3-one (d-II), as well as the unlabeled reference compound (Z)-1, 5-octadien-3-one (I) were prepared by improved synthesis procedures. Labeling position, chemical purity, and isotopic distribution of the compounds were characterized by various MS and NMR techniques. These molecules are used as internal standards in quantification experiments based on isotope dilution assay. The newly prepared compound d-II was synthesized in a simple two-step procedure, and formation of the main isotopomers was studied in model systems.