Recent literature has established that breast cancer resistance protein (ABCG2) is upregulated during lactation and is responsible for the greater than predicted accumulation of many drugs in breast milk. The objectives of this project were (1) to investigate the role of this transporter in the reported apically-directed nitrofurantoin flux in the CIT3 cell culture model of lactation, (2) to develop a mathematical model for drug transfer into breast milk to relate initial flux rates, steady-state concentrations, efflux ratios, and in vivo milk to serum ratios (M/S) and (3) to identify xenobiotic transporters that are highly expressed, and therefore potentially important for drug accumulation during lactation in mice and humans. Expression, localization, and functional assays confirmed that Abcg2 is the molecular mechanism for the apically-directed nitrofurantoin flux in CIT3 cells despite an unchanged expression level following lactogenic hormone stimulation in this model. A simple three compartment model for drug transfer into breast milk incorporating the permeability-surface area products for passive diffusion (PSD), paracellular flux (PSPC), endogenous transporters (PSB,U, PSA,E, PSB,E, and PSA,U), and ABCG2 (PSA,E(ABCG2)) transfection was developed. A stably transfected ABCG2 overexpressing MDCKII cell line was successfully created and used to explore the theoretical relationships of this new model. Derivations and correlations presented herein show the relationships between the calculated efflux ratios, PSA,E(ABCG2), and M/S attributed to ABCG2. Six xenobiotic transporters (Abcg2, Slc22a1, Slc15a2, Slc29a1, Slc16a1, and Abcc5) were identified as upregulated during lactation in murine developmental datasets analyzed by microarray expression profiling. As existing methods were inadequate to obtain pure populations of luminal epithelial cells in sufficient numbers from human breast milk or reduction mammoplasty samples for microarray analysis, a new fluorescence activated cell sorting method was developed and validated. ABCG2, SLC15A2, SLC22A12, SLC6A14, and SLCO4C1 were significantly upregulated 164-, 70-, 41-, 8-, and 2-fold during lactation, respectively. ABCC10, SLC10A1, SLC16A1, SLC22A4, SLC22A5, SLC22A9, SLC28A3, SLC29A1, SLC29A2, and SLCO4A1 had an expression level similar to, or greater than, levels in the kidney or liver. The significant upregulation of SLCO4C1 with ABCG2 is a novel finding that suggests a coordinated vectorial pathway for substrate movement into breast milk.