Cyanidin 3-glucoside (C3GLU), cyanidin 3-rutinoside (C3RUT), cyanidin 3-sambubioside (C3SAM) and cyanidin 3-(2(G)-xylosyl) rutinoside (C3XRUT) are the four constituent black raspberry anthocyanins that contribute significantly to the chemopreventive effects of freeze-dried black raspberries (FBR). A highly sensitive and specific LC-MS/MS assay was developed and validated to simultaneously quantify these four FBR anthocyanins in human saliva, plasma and oral tissue homogenates. In saliva, the lower limit of quantification (LLOQ) for these anthocyanins was 1.0 ng/mL. The within-run and between-run coefficients of variations (CVs) at the quality control concentrations (1.0, 5.0, 50 and 500 ng/mL) were all <12%, except for C3SAM and C3RUT at the LLOQ, which showed a within-run CV of 18.3% and between-run CV of 16.0%, respectively. The accuracy values ranged from 87.5 to 110%. In plasma, the LLOQ for C3GLU and C3RUT was 1.0 ng/mL and for C3SAM 5.0 ng/mL. The CVs at the above concentrations were <15%, except for C3GLU at the LLOQ, which showed the between-run CV of 16.9%. The accuracy values ranged from 90.7% to 112.7% except for C3GLU at the LLOQ, which showed 119.3%. In tissue homogenates, the LLOQ for C3GLU and C3RUT was 2.0 ng/mL, and C3SAM 5.0 ng/mL. The CVs and accuracy values at concentrations (2.0, 5.0, 50 and 500 ng/mL) were similar to those in human plasma. This assay was subsequently used in a pilot pharmacology study to evaluate the effects of topical application of a 10% (w/w) FBR bioadhesive gel to selected mucosal sites in the posterior mandibular gingiva. Measurable saliva and tissue levels of the FBR anthocyanins confirmed that gel-delivered anthocyanins are readily distributed to saliva and easily penetrate human oral mucosa.