Background Schizophrenia (SZ) and bipolar disorder (BD) are considered neurobiological disorders which share some clinical, cognitive and neuroimaging characteristics. Studying child and adolescent offspring of patients diagnosed with bipolar disorder (BDoff) or schizophrenia (SZoff) is regarded as a reliable method for investigating early alterations and vulnerability factors for these disorders. This study compares the neuropsychological characteristics of SZoff, BDoff and a community control offspring group (CC) with the aim of examining shared and differential cognitive characteristics among groups. Methods 41 SZoff, 90 BDoff and 107 CC were recruited. They were all assessed with a complete neuropsychological battery which included intelligence quotient, working memory (WM), processing speed, verbal memory and learning, visual memory, executive functions and sustained attention. Results SZoff and BDoff showed worse performance in some cognitive areas compared with CC. Some of these difficulties (visual memory) were common to both offspring groups, whereas others, such as verbal learning and WM in SZoff or PSI in BDoff, were group-specific. Conclusions The cognitive difficulties in visual memory shown by both the SZoff and BDoff groups might point to a common endophenotype in the two disorders. Difficulties in other cognitive functions would be specific depending on the family diagnosis.