The aim of investigation was to study asynchronous condensation of differentially segmented homologous chromosomes in lymphocytes of peripheral blood, as a variant of karyotype instability in families which has a children with multiple malformations and cytogenetic defects. Automatically calculated the correlation between every pair of homologous chromosomes. After that we made the correlation diagrams for all patients. Our study showed that children with multiple malformations and cytogenetic defects and their parents has low correlation of banding structure between homologs. The length and segmentation one of homologs in every pair is conform to more early condensation stage. We made a conclusion about presence of asynchronous condensation homologous chromosome. As a control we perform the same investigation of 6 families with healthy children. We found high correlation between homologous chromosomes, namely synchronous condensation homologous pairs in all patients of this group. Asynchronous condensation was found only in all members of families which has a child with cytogenetic defect.