Background: White matter abnormality has been recently proposed as a pathophysiological feature of schizophrenia (SZ). However, most of the data available has been gathered from chronic patients, and was therefore possibly confounded by factors such as duration of the disease, and treatment received. The extent and localization of these changes is also not clear. Methods: We examined a population of early stage SZ patients using diffusion tensor imaging (DTI). 77 SZ patients and 60 healthy controls (HCs) were included in the analysis using Tract-Based Spatial Statistics (TBSS). We have also analyzed 250 randomly created subsets of the original cohort, to investigate the relation between the result of TBSS analysis, and the size of the sample studied. Results: We have found a significant decrease in fractional anisotropy (FA) in the patient group. This change is present in most major white matter (WM) tracts including the corpus callosum, superior and inferior longitudinal fasciculi, inferior fronto-occipital fasciculus, and posterior thalamic radiation. Furthermore, we identified a clear trend towards an increase in the number and spatial extent of significant voxels reported, with an increasing number of subjects included in the analysis. Conclusion: Our study shows that FA is significantly decreased in patients at an early stage of schizophrenia, and that the extent of this finding is dependent on the size of studied sample; therefore underpowered studies might produce results with false spatial localization.