Studies of cholesteryl ester transfer protein (CETP) function in lipoprotein mixtures pose many difficulties by conventional biochemical methods. For instance, studies on the effects of CETP on the composition of apolipoprotein B containing lipoproteins (very low and low density lipoproteins) in lipoprotein mixtures are tedious due to repeated ultracentrifugational isolations and have thus rarely been performed. Here we present a new 1H NMR spectroscopy technique to assess the CETP function in lipoprotein mixtures. This technique does not require repeated physical isolations of the lipoprotein particles but uses mathematical separation of the fractions on the basis of biochemical prior knowledge based lineshape fitting analysis of specific lipid resonances in the 1H NMR spectra. The lipoproteins are separated according to their size related chemical shift which allows for distinct quantification between very low and low density lipoproteins, the two major apolipoprotein B containing fractions. The methodological basis of the technique is discussed here together with a demonstration that this kind of approach allows dynamic follow up of the lipid transfer reactions in complex lipoprotein and CETP mixtures. The results revealed a consistent behaviour which corroborated the recent findings suggesting that the neutral lipid mass transfer among lipoproteins is not an equimolar heteroexchange.