Pancreatectomy (Px) is known to cause islet hypertrophy and is a putative method to mimic hyperglycemia representing type II diabetes mellitus. Therefore, finding new genes related to pancreatectomy will help to understand the molecular mechanism of hypertrophy and hyperglycemia, and may provide new diagnostic markers of type II diabetes. To this end, mRNA differential display was used to isolate genes that show transcriptional changes in pancreas of rat after 90% partial pancreatectomy. Forty-nine candidate pancreas regeneration-associated transcripts were isolated. cDNA sequencing and subsequent database analysis revealed that 15 transcripts showed no significant sequence similarity to previously reported genes, whereas 34 transcripts showed significant similarity with genes deposited in the GenBank. The differential mRNA expression of 49 transcripts was confirmed using screening of slot blots and Northern blot analysis was performed to several genes. It was noteworthy that the Wnt-1 inducible signaling pathway protein-1 (WISP-1), Ras-associated protein 1B (Rap1B), vascular cell adhesion molecule-1 (VCAM-1), and huntingtin interacting protein genes (HIP) were observed to be over-expressed during pancreas regeneration. Several genes' expression was modified by pancreatectomy. Profiling of gene expression in response to pancreatectomy may lead to new insights into hypertrophy and hyperglycemia representing type II diabetes, as well as into the identification of novel diagnostic markers of type II diabetes.