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Improper dietary intake pattern in women of reproductive age in Nepal has resulted in the deficiency of essential nutrients. Adequate nutritional status and proper dietary intake pattern of women improves maternal and child health. The objective of this study was to assess the nutritional status and dietary intake pattern among the women and associated factors. Data collection at households and health check-up camps were conducted in selected Village Development Committees of nine districts in three ecological regions (Mountain, Hill and Terai) of Nepal from September 2011 to August 2012. Women of reproductive age (15 to 49 years) were the study subjects. At the household interview, structured questionnaires were used to obtain information on socio-demographic characteristics, anthropometric measurements, dietary intake pattern, consumption of junk foods, animal rearing, agricultural products, possession of kitchen garden, pregnancy status and anemia. Dietary intake pattern was determined by information collected through the structured questionnaires comprising of food items-cereals, pulses/legumes, vegetables, meat, fruits and milk and milk products. Health check-up camps were conducted in the local health facilities where qualified doctors, nurses and laboratory technicians performed physical examination of the women, confirmed their pregnancy and conducted hematocrit tests. The data was entered and analyzed using SPSS. Altogether 21,111 women were interviewed. More than a quarter of the women in Terai were malnourished as indicated by low body mass index (BMI < 18.5 Kg/m2). Among the dietary intake pattern, the majority of women consumed cereals at least once a day in all three ecological regions. The majority of women in Mountain consumed pulses/legumes thrice a week. In Terai, the majority of women consumed vegetables thrice a week. In all three ecological regions, the majority of women consumed meat and meat products and fruits once a week. About thirty percent of women consumed milk and milk products once a day in all three ecological regions. The non-use of iodized salt by Terai women was the highest (5.3 %, n = 303). In all the ecological regions, cereals and vegetables were produced in the majority of the participants’ households in comparison of fruits, poultry and goat/sheep. The women of age 15 to 24 years were 2.7 times more likely to be malnourished than women of 35 to 49 years age (aOR = 2.7, CI = 2.5,3.0). The unemployed women had nearly two times more chances of being malnourished than women doing manual work (aOR = 1.9, 95 % CI = 1.5,2.2). In Terai, women were five times more likely to be malnourished (aOR = 0.2, CI = 0.1,0.2) and 20 times more likely to be anemic (aOR = 0.05, CI = 0.04,0.07) than women in Mountain. The pregnant women were five times more likely to be anemic than non-pregnant women (aOR = 0.2, CI = 0.2,0.3). The nutritional status of women of reproductive age is still poor especially in Terai and the dietary intake pattern is not adequate. It suggests improving nutritional status and feeding habits especially intake of meat, fruits and vegetables focusing on reproductive aged women.