Endophenotypes (i.e. stable and heritable markers of the illness) are one of the promising tools to understand the pathological mechanisms underlying schizophrenia. We recently showed that deficits in visual backward masking (VBM) meet the criteria for an endophenotype. Visual masking has been proven to have much better sensitivity and specificity than other potential endophenotypes such as the continuous performance test (CPT) and the Wisconsin Card Sorting task (WCST). In addition, we found that also healthy students scoring high on cognitive disorganization have masking deficits. Interestingly, we found these effects mainly related to female students indicating a gender specific effect. To investigate whether these observations also apply to patients and relatives, VBM deficits and performance in the WCST were determined for 230 patients with schizophrenia (64 women), 102 non-affected relatives (53 women) and 82 controls (33 women). VBM deficits were worse i) in women than men and ii) in individuals high in cognitive disorganisation, assessed either in a clinical interview (patients) or with self-report questionnaires (relatives, controls). Total errors in the WCST showed a linear relationship being highest in patients followed by relatives and finally controls. While the clinical relevance of the sex difference in VBM needs to be explored, the VBM results on cognitive disorganisation point to a clinical marker in a heterogenous population that may narrow our search for possible pathological mechanisms in schizophrenia.