There is increased interest in eliminating health disparities in the United States and worldwide. Broadly defined, health disparities refer to preventable inequalities in health status, such as cancer to ethnicity, socioeconomic status, gender, education, environment, and geographic locations. To make informed health policy decisions, it is essential to precisely measure the magnitude of disparities and assess trends over time. The Health Disparities Calculator (HDCalc) is free statistical software that calculates 11 commonly used measures of health disparities and provides corresponding 95% CIs for the 11 measures using either an analytic method or a Monte Carlo simulation-based method; however, the derivation of SEs and coverage properties of the CIs have not been formally evaluated. We used simulation studies to assess the coverage properties of these CIs. We have also conducted bias analyses for measures implemented in HDCalc using age-adjusted cancer incidence rates from national, state, and county level SEER data. The results of these analyses indicate that HD*Calc should be used with caution to construct CIs for some health disparity measures when the proportion of zero event counts is greater than 25%.