Various studies have investigated reproducibility of fMRI results. Whereas group results can be highly reproducible, individual activity maps tend to vary across sessions. Individual reliability is of importance for the application of fMRI in endophenotype research, where brain activity is linked to genetic polymorphisms. In this study, the test-retest reliability of activation maps during the antisaccade paradigm was assessed for individual and group results. Functional MRI images were acquired during two sessions of prosaccades and antisaccades in twelve healthy subjects using an event-related fMRI design. Reliability was assessed for both individual and group-wise results. In addition, the reliability of differences between subjects was established in predefined regions of interest. The reliability of group activation maps was high for prosaccades and antisaccades, but only moderate for antisaccades vs. prosaccades, probably as a result of low statistical power of individual results. Reproducibility of individual subject maps was highly variable, indicating that reliable results can be obtained in some but not all subjects. Reliability of individual activity maps was largely explained by individual differences in the global temporal signal to noise ratio (SNR). As the global SNR was stable over sessions, it explained a large portion of the differences between subjects in regional brain activation. A low SNR in some subjects may be dealt with either by improving the statistical sensitivity of the fMRI procedure or by subject exclusion. Differences in the global SNR between subjects should be addressed before using regional brain activation as phenotype in genetic studies.