Accumulated evidence from a number of previous structural MRI studies have revealed 1) the existence of abnormalities even at the brain structural level in subjects at an early stage of endogeneous psychotic illness, including schizophrenia and bipolar disorder, and 2) the existence of similar brain structural abnormalities to the patients even in individuals at high-risk of endogeneous psychotic illness. Recently, an increasing number of studies have investigated the associations between the functional polymorphism of candidate genes for susceptibility to schizophrenia and regional brain volume, a highly heritable trait marker, to uncover the linkage between the candidate genes and endophenotype of schizophrenia. Firstly, this review article overviewed recent literature examining the relationship between the candidate genes for susceptibility to schizophrenia and indices obtained from neuroimaging modalities. In contrast, a relatively limited number of previous studies examined associations between candidate genes for susceptibility to bipolar disorder and regional brain volume, although the high heritability of bipolar disorder has been reported as comparable to that of schizophrenia. Then, we discussed the possibility of endophenotyping of bipolar disorder and introduced our preliminary study. Finally, methodological considerations and future directions of endophenotyping of endogeneous psychosis were suggested.