Background: Children with cleft lip and/or palate can be undernourished due to feeding difficulties after birth. A vicious cycle ensues where malnutrition and low body weight precludes the child from having the corrective surgery, in the absence of which the child fails to gain weight. This study aimed to identify the proportion of malnutrition, including the deficiency of major micronutrients, namely iron, folate and vitamin B12, in children with cleft lip and/or palate and thus help in finding out what nutritional interventions can improve the scenario for these children. Methods: All children less than 5 years with cleft lip and/or cleft palate attending our institute were included. On their first visit, following were recorded: demographic data, assessment of malnutrition, investigations: complete blood count and peripheral blood film examination; serum albumin, ferritin, iron, folate, and vitamin B12 levels. Results: Eighty-one children with cleft lip and/or palate were included. Mean age was 25.37± 21.49 months (range, 3–60 months). In 53% of children suffered from moderate to severe wasting, according to World Health Organization (WHO) classification. Iron deficiency state was found in 91.6% of children. In 35.80% of children had vitamin B12 deficiency and 23.45% had folate deficiency. No correlation was found between iron deficiency and the type of deformity. Conclusion Iron deficiency state is almost universally present in children with cleft lip and palate. Thus, iron and folic acid supplementation should be given at first contact to improve iron reserve and hematological parameters for optimum and safe surgery.