Iso-chromosome of long arm of X chromosome i(Xq), which occurs due to abnormal transverse cleavage of the centromere during cell division, found in some cases Turner Syndrome. The aim of this study is to estimate the prevalence of isochromosome X in patients with short stature with or with- out primary (PA) and secondary amenorrhea (SA) in our population. An observational study done comprised of female patients who had been referred to our cytogenetic outdoor of Vivekananda Institute of Medical Sciences (VIMS), Kolkata, India with the history of short stature with or without amenorrhoea between 2012, January-2014, December and designed as original article. The female patients aged between 10-25years having short stature with or with-out primary or secondary amenorrhea who were referred to the cytogenetic outdoor for chromosomal analysis from the departments of Pediatric medicine, Endocrinology, Gynaecology from different hospitals of Eastern India were included in the study. Lymphocyte culture depended karyo typing done using conventional method. We have documented seven such cases of is chromosome Xq among 50 female patients presented mainly with short stature with or without primary or secondary amenorrhea. Our study re-emphasizes the importance of chromosomal analysis in short stature female patients with or without primary or secondary amenorrhea to remove the diagnostic dilemma of the clinician.