Bile acids (BAs) reside in the brain and are probably involved in some neurological disorders. The view that most of unconjugated BAs in the brain are derived across the blood–brain barrier from the periphery by passive diffusion depending on their hydrophobicity is currently dominant, but some studies have made conflicting claims. In this study, the correlation analysis between the rat brain and serum levels of unconjugated BAs with a wider range of hydrophobicity was conducted to obtain further evidence about the blood-to-brain influx of unconjugated BAs by passive diffusion. We first developed the precise, accurate and matrix effect-free LC/ESI-MS/MS methods for quantifying eight major unconjugated BAs in the rat brain and serum. Derivatization was employed for increasing the assay sensitivity and specificity. The analysis using these methods reproduced the strong positive correlations between the brain and serum levels, and significant higher concentrations in the serum than in the brain for all the unconjugated BAs. The BA with the higher logPow (hydrophobicity) had the higher brain-to-serum concentration ratio (mono- > di- > trihydroxy BAs). Furthermore, the hydrophobicity was considered as the stronger factor for the blood-to-brain influx of the BAs than the serum protein binding ratio. Thus, this study provided further evidence supporting that passive diffusion is the major mechanism for the blood-to-brain influx of the unconjugated BAs.