The comet assay is widely used to detect DNA damage in single cells. However, only moderate attention has been paid to the experimental variability of this assay, especially during electrophoresis. To take into account this variation and to be able to compare measurements from different electrophoretic runs, as would be necessary when large numbers of samples need to be analysed, it is important to integrate an internal standard into the assay. This study presents a first step in the validation and implementation of an internal standard in the alkaline comet assay. Untreated and ethyl methanesulfonate treated cells (K562 human erythroleukemia cell line) were used as negative and positive internal standards, respectively, in each electrophoresis run. Three steps were followed: (1) assessment of the different levels of variability which may influence the damage levels of the internal standards, (2) evaluation of the variability across separate electrophoresis runs on the quantification of DNA damage in the internal standards by three experimenters involved in different studies and (3) proposal of an adequate calculation system to integrate the internal standards into test sample data. The application of the two proposed models to samples from a human biomonitoring study is presented. The model which calibrates the measurements against the negative internal standard is the most useful since this negative standard was the most stable across experiments and among the three experimenters. The percentage of DNA in the tail is the most appropriate parameter to analyse induced DNA damage, because its interelectrophoresis and interexperimenter variation is less pronounced than that of tail length.