To date there is no anthropometric equation specific to athletes with unilateral lower limb amputation to estimate the percentage of fat mass (%FM). This study investigated the accuracy of a set of anthropometric equations validated on able-bodied populations to predict the %FM assessed by-means of dual-energy x-ray absorptiometry (DXA) in athletes with unilateral lower limb amputation. Furthermore, a predictive anthropometric equation specific to athletes with unilateral lower limb amputation was developed from skinfold thickness measurements using DXA as the reference method for the estimation of the %FM. Twenty-nine white male athletes with unilateral lower limb amputation underwent a DXA scan and an anthropometric assessment on the same day. The %FM, calculated through several existing anthropometric equations validated upon able-bodied populations, was compared with the DXA-measured %FM (%FM_DXA). Accuracy and agreement between the two methods was computed with two-tailed paired-sample t-test, concordance correlation coefficient, reduced major axis regression and Bland-Altman analysis. A stepwise multiple regression analysis with the %FM_DXA as the dependent variable and age and nine skinfold thicknesses as potential predictors was carried out and validated using a repeated 10-fold cross-validation. A linear regression analysis with the sum of nine skinfolds as the independent variable was also carried out and validated using a repeated 10-fold cross-validation. The results showed that the anthropometric equations validated on able-bodied populations are inaccurate in the estimation of %FM_DXA with an average bias ranging from 0.51 to -13.70%. Proportional bias was also found revealing that most of the anthropometric equations considered, tended to underestimate/overestimate the %FM_DXA as body fat increased. Regression analysis produced two statistically significant models (P < 0.001 for both) which were able to predict more than 93% of total variance of %FM_DXA from the values of four skinfold measurements (i.e., thigh, abdominal, subscapular and axillary skinfold measurements) or from the sum of 9 skinfolds. Repeated cross-validation analysis highlighted a good predictive performance of the proposed equations. The predictive equations proposed in this study represent a useful tool for clinicians, nutritionists, and physical conditioners to evaluate the physical and nutritional status of athletes with unilateral lower limb amputation directly in the field.