Objectives This study analyze the correlation between iris markings and the obesity level shown in body composition indices. And It quantitatively evaluates iris markings according to the level of obesity to improve a clinical application plan for the iris analysis. Methods This study analyzed the iris and body composition through the quantization of iris markings for 28 female patients. It calculated descriptive statistics by using SPSS 13.0 and investigated correlation coefficients of non-parametric Spearman in order to analyze the relation between iris markings and body composition indices. Results Considering the correlation between iris markings and body composition indices, an area of the pupil had a significant positive correlation with height and with fat-free amount such as body water, protein, and minerals. BMI showed significant positive correlations with the length of the autonomic nerve wreath and the ratio of the autonomic nerve wreath, and the area of the autonomic nerve wreath. Moreover, the number of lacunas in the pancrea area had a significant positive correlation with weight and BMI. Conclusions This study objectifies the quantification of iris markings to identify the correlation between iris markings and the level of obesity. The study results will be used as a basic data to make standards for the diagnosis of obesity, the treatment of related diseases, and the diagnosis of iris markings for prevention.