We have investigated the segmental and crypt-villus distribution of ABC (ATP-binding cassette transporter) mRNA’s (mdr1a, (abcb1a); mrp2, (abcc2); and bcrp, (abcg2)) involved in protection of rat intestine from xenobiotic uptake. Male Sprague-Dawley rats were killed by cervical dislocation and their intestines excised and washed in ice-cold Liebovitz + L-glutamine medium. Mucosal scrapes were taken from duodenum, jejunum, ileum and distal colon. Enriched ileal villus tip and crypts were prepared using a modified Weisser technique [1]. Ileum was inverted and vibrated in an EDTA-containing solution to give villus tips (fractions 1 and 2) and later crypts (f9 and 10) [1].Both mucosal scrapes and pelleted villus tip/crypt fraction samples were rapidly frozen at -80oC and total RNA subsequently isolated from 30mg samples using Qiagen mini-plus isolation protocols. RNA integrity values (RIN) were >6, except for duodenal samples where 260/280nm ratios were used. Multiplexed measurement of target gene expression was made using NanoString technology where hybridization of gene-specific target and bar-coded capture probes allows direct quantification using the nCounter™ Analysis System [2]. Normalisation of mRNA levels for RNA concentration using 4 housekeeping genes (gapdh, villin, hmbs and hrpt1) showed bcrp mRNA expression levels (duodenum; 27.96 ± 3.05 fmol/sample, jejunum; 28.82 ± 2.86 fmol, ileum; 42.26 ± 10.27 fmol, colon; 31.0 ± 2.03 fmol) to exceed that of mdr1a (duodenum; 3.35 ± 0.7 fmol, jejunum; 4.19 ± 0.83 fmol, ileum; 9.61 ± 2.6 fmol, colon; 8.08 ± 1.84 fmol) and mrp2 (duodenum; 9.40 ± 2.46 fmol, jejunum; 12.56 ± 3.44 fmol, ileum; 9.87 ± 5.44 fmol, colon; 0.49 ± 0.24 fmol) (n=3, ± SEM) in all four intestine segments. Increased mRNA expression for both bcrp and mdr1a was shown along the length of the small intestine (duodenum to ileum) with lower mRNA expression being apparent in the colon. The Mrp2 expression profile was jejunum > ileum = duodenum >>colon. NanoString analysis of villus and crypt preparations showed significant concentration of proliferating cell nuclear antigen (PCNA) and nkcc1 (slc12a2) in the crypts (log2 villus: crypt ratios, -1.66 ± 0.272 (p=0.004 vs 1, T-test) and -2.88 ± 0.58 (p=0.006) respectively, n=3 ± SEM. In contrast, leucine aminopeptidase and alkaline phosphatase mRNA showed enhanced expression in the villus tip (log2 villus: crypt ratio, 2.35 ± 0.19 (p=0.001) and 3.08 ± 9.0 (p=0.03), n=3 ± SEM). Bcrp, mdr1a, and mrp2 showed villus: crypt mRNA ratios of 1.66 ± 0.16 (p=0.03), 1.92 ± 0.21 (p=0.054) and 2.10 ± 0.33 ( p=0.006) (n=3 ± SEM). Bcrp transporter mRNA is thus present in both crypt and villus cells and bcrp protein may function in protection of crypt stem cells from xenobiotic insult.