We present a general scheme for metabolite quantification from a two-dimensional (2D) (1)H-(13)C heteronuclear single quantum correlation (HSQC) nuclear magnetic resonance (NMR) experiment of body fluids observed in natural abundance. The scheme of quantification from 2D HSQC spectra consists of measurement of relaxation parameters of proton resonances, such as T(1) and T(2) of the metabolites and (1)H-(13)C heteronuclear J-coupling for accurate quantification. The measured cross-peak volume from 2D HSQC NMR spectra is multiplied by a calculated correction factor (which depends upon two-dimensional NMR experimental parameters and relaxation parameters) to measure accurate quantification of the metabolite. The correction factor is theoretically derived from the solution of the Bloch equation and product operator formalism. The accuracy of the scheme is tested on a solution containing a mixture of amino acids of known concentration. For human urine samples, the accuracy of the method for measuring the concentration of various metabolites was tested with spike-in experiments. The scheme is general in nature and can be applied to any other body fluid samples for metabonomic studies. We also test the measured cross-peak volume of various metabolites from 2D (1)H-(13)C HSQC NMR spectra of human urine samples for clustering analysis with scatter plots, making the scheme complete for metabolic profiling.