Factors affecting the accuracy of the analysis of lignin hydroxyl and carboxyl groups with P-31 NMR have been further elucidated. Two modifications of P-31 NMR analysis of lignin, namely the protocols using 1,3,2-dioxaphospholane (PR-I) and 2-chloro-4,4,5,5-tetramethyl-,3,2-dioxaphospholane (PR-II) as phosphorylation reagents with different internal standards, were studied. The previous P-31 NMR standard protocol with PR-II underestimated OH groups by about 30%, whereas the P-31 NMR standard protocol with PR-I tended to produce overestimated data. It has been shown that cholesterol is not an appropriate internal standard, resulting in underestimated values for OH groups due to incomplete baseline resolution. The best internal standard has been found to be endo-N-hydroxy-5-norbornene-2,3-dicarboximide. Strong care should be taken related to the stability of the internal standards to avoid inflated results due to IS degradation. Under modified optimized conditions, both methods show a good correlation with the C-13 NMR protocol in the quantification of hydroxyl groups as average, with the variability between the methods in the range of 5-15%. However, the P-31 NMR protocols report COOH content that is twice as low as that of C-13 NMR data. Finally, the best approach for the use of the P-31 and C-13 NMR methods in lignin analysis is discussed.