Background: The objective of the study was to assess hair trace element and mineral content in children undergoing WFP UN and the governmental programs of school nutrition in Tajikistan. Methods: WFP program included provision or wheat flour fortified with micronutrients including Fe and Zn, and iodized salt, whereas within the governmental program hot meals were provided. A total of 202 children studying in schools that were not (Type 1, n = 100) or were involved in dietary intervention programs (Type 2, n = 102). Food and hair trace element content was assessed using ICP-MS. Results: Daily intake of Fe, I, Zn, B, Co, Mg, Si, and Sr in Type 2 schools was more than 2.5, 12, 4, 2.9, 2.6, 2, 3, and 2-fold higher than that in Type 1 schools. Correspondingly, anthropometric parameters in children from Type 2 schools exceeded the control values. Surprisingly, no significant difference in hair iodine levels was detected. Hair analysis demonstrated a significant increase in hair Ca, Mg, Na, Co, Cr, Cu, Fe, Li, Mn, Se, V, Zn content. Certain toxic elements including Al, As, and Be were also characterized by an increase in Type 2 schools. At the same time, nutritional intervention was associated with a significant decrease in hair B, Hg, and Sn levels. Conclusions: Nutritional intervention within WFP and the governmental program was effective in increasing essential trace element supply in Tajik schoolchildren. However, further studies including a detailed assessment of nutritional and health status with a special focus on iodine and thyroid functioning are required. © 2019 Elsevier GmbH