A pharmacokinetic model was constructed to explain the difference in brain-and cerebrospinal fluid (CSF)-to-plasma and brainto-CSF unbound drug concentration ratios (K p,uu,brain , K p,uu,CSF , and K p,uu,CSF/brain , respectively) of drugs under steady-state conditions in rats. The passive permeability across the blood-brain barrier (BBB), PS 1 , was predicted by two methods using log(D/molecular weight 0.5 ) for PS 1 (1) or the partition coefficient in octanol/water at pH 7.4 (LogD), topologic van der Waals polar surface area, and van der Waals surface area of the basic atoms for PS 1 (2). The coefficients of each parameter were determined using previously reported in situ rat BBB permeability. Active transport of drugs by P-glycoprotein (P-gp) and breast cancer resistance protein (Bcrp) measured in P-gp-and Bcrp-overexpressing cells was extrapolated to in vivo by introducing scaling factors. Brain-and CSF-toplasma unbound concentration ratios (K p,uu,brain and K p,uu,CSF , respectively) of 19 compounds, including P-gp and Bcrp substrates (daidzein, dantrolene, flavopiridol, genistein, loperamide, quinidine, and verapamil), were simultaneously fitted to the equations in a three-compartment model comprising blood, brain, and CSF compartments. The calculated K p,uu,brain and K p,uu,CSF of 17 compounds were within a factor of three of experimental values. K p,uu,CSF values of genistein and loperamide were outliers of the prediction, and K p,uu,brain of dantrolene also became an outlier when PS 1 (2) was used. K p,uu,CSF/brain of the 19 compounds was within a factor of three of experimental values. In conclusion, the K p,uu,CSF/brain of drugs, including P-gp and Bcrp substrates, could be successfully explained by a kinetic model using scaling factors combined with in vitro evaluation of P-gp and Bcrp activities.