Previous researches reported that the command signals, including pulse and step, are generated in the brain stem and activates the oculomotor neurons for saccade generation. It was discovered that disorder of these two components will cause abnormal saccades. Recently independent component analysis (ICA) has been used in the decomposition of biomedical signals. In one investigation, ICA was used for successfully decomposing the transient and sustained components of the vergence eye movements. In this study, we applied ICA to decompose the pulse and step signals from the recorded saccadic profiles. Nine normal young subjects (mean age: 24.7) and three patients, including two (age: 57 and 55) with brainstem lesions and one (age: 44) with bilateral calcification over basal ganglia were tested for this investigation. The results show that the pulse and step components can be accurately decomposed from the saccadic ensemble profiles using ICA for both normal and patient subjects. It also demonstrates that the decomposed pulse duration for the patients is significantly elongated than the normal subjects. To compare the patients with brain stem lesions to a patient with bilateral calcifications over basal ganglia, it was found that the saccadic performance is not affected for the latter, which is consistent with previous findings that brain stem is responsible for the generation of saccadic commands.