Subacute rumen acidosis (SARA) is a significant concern in dairy cattle fed grain-rich diets. To elucidate the underlying pathophysiological mechanisms, ruminal papilla biopsies are often used. This study aimed to assess how the sampling site along the ruminal papilla influences gene expression profiles in rumen epithelium during SARA. Rumen biopsies from five ruminal-cannulated non-lactating Holstein cows were collected during feeding of a forage diet (FD) and seven (wk1) and 21 days (wk3) after transition to high-grain (HG) feeding. Gene expression in apical (AP), basal (BP), and total length (TP) papillae were compared using RT-qPCR. Significant diet-induced effects were observed in AP for DSG1 (wk3, p = 0.0317), ZO1 (wk1 and wk3, p = 0.0159), GLUT3 (wk3, p = 0.0159), TLR4 (wk3, p = 0.0635), and NFKB (wk1, p = 0.0159), but hardly in BP or TP. Within wk1, TP showed higher transcript levels of ZO1 and TLR4 (p = 0.0079) and SGLT1 (p = 0.0317) compared to AP and BP independently from diet effects. These findings suggest that the apical parts of rumen papillae biopsies are most suitable for gene expression analyses to investigate diet-induced effects on rumen physiology and underscore the importance of considering the sampling site for accurate gene expression studies in rumen epithelium during SARA, providing valuable insights for future research and diagnostic approaches in managing rumen health in dairy cattle.