Autism Spectrum Disorders (ASD) and Williams Syndrome (WS) are complex cognitive conditions exhibiting quite opposite features in the social domain: whereas people with ASD are mostly hyposocial, subjects with WS are usually reported as hypersocial. At the same time, ASD and WS share some common underlying behavioral and cognitive deficits. It is not clear, however, which genes account for the attested differences (and similarities) in the socio-cognitive domain. In this paper we adopted a comparative-molecular approach and looked for genes that might be differentially (or similarly) regulated in the blood of people with these conditions. We found a significant overlap between genes dysregulated in the blood of patients compared to neurotypical controls, with most of them being upregulated or, in some cases, downregulated. Still, genes with similar expression trends can exhibit quantitative differences between conditions, with most of them being more dysregulated in WS than in ASD. Differentially-expressed genes are involved in aspects of brain development and function (particularly, dendritogenesis) and are expressed in brain areas (particularly, the cerebellum, the thalamus and the striatum) of relevance for the ASD and the WS etiopathogenesis. Overall, these genes emerge as promising candidates for the similarities and differences between the ASD and the WS socio-cognitive profiles.