Estimating stature is essential in the process of personal identification. Because it is difficult to find human remains intact at crime scenes and disaster sites, for instance, methods are needed for estimating stature based on different body parts. For instance, the upper and lower limbs may vary depending on ancestry and sex, and it is of great importance to design adequate methodology for incorporating these in estimating stature. In addition, it is necessary to use machine learning rather than simple linear regression to improve the accuracy of stature estimation. In this study, the accuracy of statures estimated based on anthropometric data was compared using three imputation methods. In addition, by comparing the accuracy among linear and nonlinear classification methods, the best method was derived for estimating stature based on anthropometric data. For both sexes, multiple imputation was superior when the missing data ratio was low, and mean imputation performed well when the ratio was high. The support vector machine recorded the highest accuracy in all ratios of missing data. The findings of this study showed appropriate imputation methods for estimating stature with missing anthropometric data. In particular, the machine learning algorithms can be effectively used for estimating stature in humans.