We studied the variability in saccades by comparing the peak velocities of saccades with the same target amplitude made with different actual amplitudes. We tested three hypotheses namely: 1) the pulse height noise hypothesis (peak velocity and amplitude vary proportionally), 2) the localization noise hypothesis (variability in amplitude and peak velocity lie along the main sequence), and 3) the independent noise hypothesis (variability in amplitude and peak velocity are independent). We measured eye orientation in two experiments by a scleral coil and a video system. Surprisingly, the main source of variability of saccades depended on the measurement system used. A combination of localization noise and independent noise best describes the data obtained by the video system. The independent noise (e.g. measurement inaccuracy) was the main source of variability. For the scleral coils, the variability was considerably larger than for the less accurate video system. The pulse-height noise hypothesis best describes this additional variability. Therefore, we conclude that pulse-height noise is the main source of variability in saccades measured with scleral coils. We discuss the influence of scleral coils on saccade generation, and suggest that a change in motor strategy due to the discomfort of wearing the coils might be the cause of the increased variability.