North Korean defectors who settle in South Korea have experienced severe food shortage and transition of food environment which could affect their health status. However, little is known about their anthropometric measurements and dietary intake after settlement in South Korea. The purpose of this study is to compare anthropometric measurements and dietary intake between North Korean young adults who defected to South Korea and those of South Koreans. We hypothesized that North Korean young adults' physiques and dietary intake would be poorer than that of South Koreans. We compared anthropometric measurements and dietary intake from 3-day food records in a cross-sectional study of 103 North Korean young adult defectors, aged 12 to 24 and 309 South Korean subjects. North Korean subjects were significantly shorter (4.9 to 10.8 cm) and lighter (6.0 to 12.5 kg) than the control group. Body mass index were significantly different between North and South Korean groups only in men. North Korean young adult defectors had lower mean daily intakes of energy and most nutrients and food groups compared to the control group, while North Korean subjects had higher nutrient density diet than that of South Koreans. The proportion of subjects who had dietary intakes of nutrients of less than the Estimated Average Requirement was higher in North Korean subjects than in controls except for in the cases of vitamin A and vitamin C. In conclusion, we recommend providing nutrition support programs for North Korean young adult defectors to secure adequate nutrient intake.