Objective: To evaluate anemia and related nutritional status of 6-17 years old boarding school students in rural areas of central and western China, and to reveal the difference of nutrition problems in different regions. Methods: In the central and western regions, Henan, Anhui, Jiangxi, Guangxi and Sichuan provinces, as well as Tibet Autonomous Region were selected for this survey considering similar per capita GDP levels. One secondary school and one primary school which participated in the National Nutrition Improvement Program for Rural Compulsory Education Students were selected from each province. One class was selected from each grade of every school by using cluster sampling method. A total of 2 180 students were selected in this survey. Venous blood was collected and the level of hemoglobin, ferritin, soluble transferrin receptor, folic acid and vitamin B12 was analyzed to evaluate anemia and nutrient deficiencies. Results: As for western region, prevalence of anemia among students aged 6-8 and 9-11 years was 3.2% and 2.9%, respectively; iron deficiency prevalence among students aged 6-8, 9-11 and 12-14 years was 10.8%, 13.8% and 24.3%, respectively; and folic deficiency prevalence among students aged 12-14 and 15-17 years was 32.7 % and 49.4%, respectively. Prevalence of anemia, iron and folic deficiency in those areas was significantly higher than those of central regions (all P <0.05). As for the central regions, vitamin B12 deficiency prevalence of students aged 6-8, 9-11, 12-14 and 15-17 years was 7.3%, 19.4%, 29.2% and 45.5% respectively, which was significantly higher than of those of the western regions at the same age group. Conclusion Anemia, iron deficiency and folic acid deficiency are more common among students in western region, while the vitamin B12 deficiency problem is more common in central region. There are regional differences in the nutritional problems of students in the rural areas of central and western part of China. Nutrition improvement of student needs to be adapted to local conditions.