In this paper, we studied a dataset composed of 159 anatomical MR images pooled from three different scanners, including 75 ASD patients and 84 healthy controls. We quantitatively assessed the effects of the age, pathology and scanner factors on cortical thickness measurements. We observe that the effect size associated to the scanner factor is larger than the effect of pathology in almost every cortical region. Moreover, while the effect of age is consistent across scanners, the interaction between the age and scanner factors is important and significant in some specific cortical areas. Our results allow for a better understanding of the frequent discrepancies observed in the literature of ASD. We conclude that maximizing the consistency of image characteristics across scanners is mandatory for multi-site quantitative MRI studies in the context of neuro-developmental pathologies such as ASD.