Estimates of the effective dose to adult patients from computed tomography (CT) head scanning can be calculated using a number of different methods. These estimates can be used for a variety of purposes, such as improving scanning protocols, comparing different CT imaging centers, and weighing the benefits of the scan against the risk of radiation-induced cancer. The question arises: What is the uncertainty in these effective dose estimates? This study calculates the uncertainty of effective dose estimates produced by three computer programs (CT-EXPO, CTDosimetry, and ImpactDose) and one method that makes use of dose-length product (DLP) values. Uncertainties were calculated in accordance with an internationally recognized uncertainty analysis guide. For each of the four methods, the smallest and largest overall uncertainties (stated at the 95% confidence interval) were: 20%-31% (CT-EXPO), 15%-28% (CTDosimetry), 20%-36% (ImpactDose), and 22%-32% (DLP), respectively. The overall uncertainties for each method vary due to differences in the uncertainties of factors used in each method. The smallest uncertainties apply when the CT dose index for the scanner has been measured using a calibrated pencil ionization chamber.