The expression of subunits of the guanine nucleotide regulatory protein that mediates hormonal stimulation of adenylyl cyclase (G(s)) and of the guanine nucleotide regulatory protein that mediates hormonal inhibition of adenylyl cyclase (G(i)) was studied during cell migration and differentiation in the rat small intestine crypt-villus axis. Proliferative crypt cells were separated from nonproliferative mature villus cells and the following data were obtained: 1) alpha(s) subunits were more abundant in crypt cells than in villus cells as evidenced by cholera toxin-catalyzed [P-32]NAD ribosylation and Western blotting of this relative molecular weight (M(r)) 42,000 protein; 2) alpha-i2- and alpha-i3-subunits (M(r) 40,000 and M(r) 41,000, respectively) were preferentially expressed in villus cells as evidenced by pertussis toxin-catalyzed [P-32]NAD ribosylation and Western blotting (alpha-i1subunit was not detectable in intestinal epithelium by using these techniques); 3) Western blotting showed a higher expression of the common beta- (M(r) 36,000) subunit of G proteins in villus cells than in crypt cells; and 4) Northern blot analysis using an alpha(s)-subunit oligonucleotide probe showed a 1.9-kb mRNA that was more abundant in crypt cells than in villus cells. In contrast, alpha-i2- and alpha-i3-mRNA species (2.3 and 3.5 kb, respectively), analyzed by using specific cDNA probes, were much more abundant in villus cells than in crypt cells. Finally, two beta-subunit mRNA species of 3.3 and 1.8 kb were detectable in intestinal epithelial cells and were more abundant in villus cells than in crypt cells. It was concluded that G(s) and G(i) protein subunits undergo divergent expression during epithelial cell differentiation in the small intestine crypt-villus axis. The gradients of expression of G protein subunits appear to be generated by control of their mRNA levels.