Intranuclear rodlets (INRs) are structures present within the nuclei of human insulin-secreting beta cells of the endocrine pancreas. Their physiological significance, and whether they are altered in disease, is unknown. In the present study, the proportion of pancreatic beta cells containing INRs was examined in mouse models of type II diabetes and in a model with improved beta cell function. To gain insights into the molecular regulators of INR formation, mice with a conditional adult beta cell-specific knockout of the serine/threonine protein kinase Lkb1 (Lkb1 adult beta cell knockout (LABKO) mice) were studied. To investigate INR changes in a pathophysiological context, beta cell INRs were examined in two models of human metabolic syndrome: (1) mice maintained on a high-fat diet and (2) leptin-deficient ob/ob mice. The proportion of beta cells containing INRs was significantly reduced in LABKO mice. This reduction was not mediated by two key downstream effectors of Lkb1, mTor and Mark2. High-fat diet regimen reduced beta cell INR frequency by more than 40%, and leptin-deficient ob/ob mice exhibited a dramatically (19-fold) reduced INR frequency relative to wild-type mice. Taken together, our results support the view that INR formation in pancreatic beta cells is a dynamic and regulated process. The substantial depletion of beta cell INRs in LABKO and diabetic mice suggests their relationship to beta cell function and potential involvement in diabetes pathogenesis.