Microanalytical methods were developed for measuring galactosyl-beta-cyclodextrin (Gal-betaCD) and mannosyl (Man)-betaCD in biological matrices of the rat by HPLC with pulsed amperometric detection. Then, using these methods, the absorption, distribution and excretion of intravenously and orally administered Gal-betaCD and Man-betaCD were determined in rats, and compared with those of glucosyl (Glc)-betaCD. The pharmacokinetic behavior of Gal-betaCD, Man-betaCD and Glc-betaCD after intravenous administration (50 mg/kg) was very similar. Within 6 h after intravenous administration, unchanged Gal-betaCD and Man-betaCD recovered in urine accounted for about 90% of each dose. After oral administration (500 mg/kg), 0.37% and 0.38% of Gal-betaCD and Man-betaCD, respectively, were excreted in urine. After intravenous and oral administration of Gal-betaCD and Man-betaCD, the decomposition of Gal-betaCD and Man-betaCD to betaCD in the urine, kidney and liver was greater than that of Glc-betaCD. The sum of the molar concentrations of branched CDs and their decomposition product, betaCD, in the liver at 4 h after intravenous administration of Gal-betaCD and Man-betaCD was greater than that of Glc-betaCD. Furthermore, the inclusion complexes of estriol and betamethasone with Gal-betaCD, Man-betaCD and Glc-betaCD were prepared and their absorption was evaluated after oral administration in rats. The plasma concentrations of the drugs after oral administration of drug-Gal-betaCD and drug-Man-betaCD complexes were the same as those after the administration of drug-Glc-betaCD complexes.