High-fat, low-carbohydrate ketogenic diets (KD) are used for weight loss and for treatment of refractory epilepsy. Recently, short-time studies in rodents have shown that besides their beneficial effect on body weight, KD lead to glucose intolerance and insulin resistance. However, the long-term effects on pancreatic endocrine cells are unknown. In this study we investigate the effects of long-term KD on glucose tolerance and beta and alpha cell mass in mice. Despite an initial weight loss, KD did not result in weight loss after 22 weeks. Plasma markers associated with dyslipidemia and inflammation (cholesterol, triglycerides, leptin, MCP-1, IL-1β and IL-6) were increased and KD-fed mice showed signs of hepatic steatosis after 22 weeks of diet. Long-term KD resulted in glucose intolerance that was associated with insufficient insulin secretion from beta cells. After 22 weeks insulin-stimulated glucose uptake was reduced. A reduction in beta cell mass was observed in KD-fed mice together with an increased number of smaller islets. Also alpha cell mass was markedly decreased, resulting in a lower alpha to beta cell ratio. Our data show that long-term KD causes dyslipidemia, a pro-inflammatory state, signs of hepatic steatosis, glucose intolerance and a reduction in beta and alpha cell mass, but no weight loss. This indicates that long-term high-fat, low-carbohydrate ketogenic diets lead to features that are also associated with the metabolic syndrome and an increased risk for type 2 diabetes in humans.