The determination and separation of bases from the degradation products of DNA in hydrochloric acid, perchloric acid, trichloroacetic acid, trifluoroacetic acid and formic acid were described. The hydrolysis yields of DNA adduct products of MNU also were presented. The effects of mobile phase composition, flow rate, column temperature, gradient ramp, pH value, salt concentration, and buffered concentration on capacity factors (K-1) were respectively discussed. The experimental results showed that hydrochloric acid is a favorable hydrolytical medium for DNA degradation and high recovery of DNA bases can be obtained. The optimum hydrolytical conditions for adduct products of DNA of MNU were 1 mol/L hydrochloric acid, 20 min, and 80-100 degree C.