Background: Iron deficiency anemia is the most common nutritional deficiency of world affecting people of all ages and economic groups. Previous studies on the effects of iron deficiency anemia by exfoliative oral cytology have produced conflicting results but application of quantitative parameters such as nuclear diameter (ND) and cytoplasmic diameter (CD) and nuclear to cytoplasmic ratio (N/C) has shown to be significant in the diagnosis of oral lesions. The present study was undertaken to assess the morphometric changes in CD and ND of squames obtained from buccal mucosa of patients with iron deficiency anemia and also to assess the effect of serum ferritin levels on cellular morphometry. Materials and Methods: Thirty cases of iron deficiency anemia and 30 cases of control group were selected for the study. The control group consisted of people without clinical symptoms of anemia, normal hematological and serum ferritin levels. Scrapings were taken from the buccal mucosa of the iron deficiency anemia patients and control groups and stained with Papanicolaou stain. ND and CD were measured using image analyzer. Results: CD and ND values of the control group were found to be in the range of 65.32-75.39 μ and 8.10-9.40 μ respectively. CD values of iron deficiency were 55.05-64.12 μ with the mean CD value of 59.77 μ and ND values were 8.69-11.24 μ with mean ND values of 9.88 μ. On correlating the serum ferritin and red cell parameters with the CD and ND values of iron deficiency anemia showed positive correlation. Conclusions: The decrease in cytoplasmic diameter and increase in ND in iron deficiency anemia and progressive decrease in CD with decrease in serum ferritin levels suggested that iron deficiency causes significant changes in oral exfoliative cells. Cytomorphometric analysis of smears is useful in detecting the changes in iron deficiency anemia.