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Alzheimer’s disease (AD) has as its core attribution in the decline of cerebral functions. Though, its etiology complex a perceptive is made for understanding its neurological, infectious, biochemical, genetic and cytogenetic mechanisms. Considering this, the study aimed to investigate the presence of chromosomal alterations in the peripheral blood lymphocytes and the genetic polymorphism of APO E was investigated using the PCR-RFLP technique also to verify if there was a high frequency of these alterations in patients diagnosed with AD, cardiovascular disease (CVD) and control. A total of 60 subjects, corresponding to 20 AD, 20 CVD and 20 controls were recruited for this study from Hospitals in Coimbatore. The mean ± SD values of chromatid type aberrations (CTAs) and chromosomal type aberrations (CSAs) for AD, CVD and control subjects were studied CTAs, CSAs and CA level of CVD subjects shows higher when compared to AD and control subjects. Therefore, the karyotypes of patients with AD, CVD undergo chromosomal alterations at different levels and they emphasize the importance in these cytogenetic investigations the routine management along with the association between CVD risk and AD. Carriers harbouring APO E E4/E4 mutations are at higher risk of disease and those with the APO E E3/E4 lowest risk, who represent the bulk of families with Alzheimer’s disease, typically harbour gene mutation.