The study was designed to confirm the diagnosis of Fanconi Anemia patients by MMC induced chromosomal breakage studies along with the related clinical characteristics at cytogenetic laboratory of Armed Forces Institute of Pathology, Rawalpindi. Out of 192 patients included in the study, 24 had confirmed diagnosis of Fanconi anemia. Amongst which 14 (58.33%) were male and 10 (41.66 %) were female patients. The mean age calculated for this disease in our study is 11.18 years. These patients presented with phenotypic features like hyperpigmented spots on skin, microcephaly, short stature or thumb/radial anomalies. Many suffered from aplastic anemia while some had pancytopenia, thrombocytopenia or less frequently prevalent bone marrow disorders. Major characteristics noted in the present study were the anomalies related to weight, height and skeleton. Leukemia or Myelodysplastic syndrome was also present in some of the cases. Moreover, they had other clinical history of bruises, infections, bleeding gum and fever etc. Around 30-50% of the metaphases showed breakages in the chromosomes of these after being subjected to clastogenic stress by mitomycin C. The cytogenetic analysis pattern of Fanconi anemia is like the international studies. At present, the technique mentioned in our study using the mitomycin C (MMC) induced chromosome instability is the gold standard test for the timely diagnosis of Fanconi anemia as clinical features cannot confirm the diagnosis alone. With the use of DNA cross linking clastogenic chemicals such as Mitomycin-C (MMC); the diagnosis and timely confirmation of this disease can be done when patients presented with related signs and symptoms. Early diagnosis of this disorder is very important as this would help in efficient treatment of patients before the disease starts showing further life-threatening complications. Knowing the karyotype pattern of Fanconi anemia can also help in genetic counseling of the patients and their families. Also, wide-scale national community-based survey with Fanconi anemia registry could help in estimating the size of the problem in our country more accurately as previously no such work has been done or available in the literatures.