Ghrelin secretion has been associated with increased caloric intake and adiposity. The expressions of ghrelin and its receptor (GHS-R1a) in pancreas have raised the interest about the role of ghrelin in glucose homeostasis. Most of the studies showed that ghrelin promoted hyperglycaemia and inhibited insulin secretion. This raised the interest in using GHS-R1a antagonists as therapeutic targets for type 2 diabetes. Available data of GHS-R antagonists are on a short-term basis. Moreover, the complexity of GHS-R1a signalling makes it difficult to understand the mechanism of action of GHS-R1a antagonists. This study examined the possible effects of long-term treatment with a GHS-R1a antagonist, [D-Lys3]-GHRP-6 on glucose homeostasis, food intake and indirect calorimetric parameters in non-obese diabetic MKR mice. Our results showed that [D-Lys3]-GHRP-6 (200nmol/mouse), reduced pulsatile growth hormone secretion and body fat mass as expected, but worsened glucose and insulin intolerances and increased cumulative food intake unexpectedly. In addition, a significant increase in blood glucose and decreases in plasma insulin and c-peptide levels were observed in MKR mice following long-term [D-Lys3]-GHRP-6 treatment, suggested a direct inhibition of insulin secretion. Immunofluorescence staining of pancreatic islets showed a proportional increase in somatostatin positive cells and a decrease in insulin positive cells in [D-Lys3]-GHRP-6 treated mice. Furthermore, [D-Lys3]-GHRP-6 stimulated food intake on long-term treatment via reduction of POMC gene expression and antagonized GH secretion via reduced GHRH gene expression in hypothalamus. These results demonstrate that [D-Lys3]-GHRP-6 is not completely opposite to ghrelin and may not be a treatment option for type 2 diabetes.