Haematological cancers like leukemia and lymphoma are characterized by genetic abnormalities, specifically chromosomal translocations. Analyses of the translocation breakpoint regions in patients have shown that some loci in the genome are more susceptible to breakage than others. However, very little is known about the mechanism of generation of many such chromosomal translocations. In the present study, we have attempted to understand the mechanism of fragility of three regions, which are prone to breaks during translocations in follicular lymphoma (FL) and T-cell leukemia. The t(14;18) translocation in FL is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3’ UTR of the BCL2 gene and are broadly classified into three clusters, namely major breakpoint region (mbr), minor breakpoint cluster region (mcr) and the intermediate cluster region (icr). The RAG complex has been shown to cleave BCL2 mbr by recognizing an altered DNA structure. In the present study, by using a gel based assay, nature of the non-B DNA structure at BCL2 mbr was identified as parallel intramolecular G-quadruplex. Various studies including circular dichroism (CD), mutagenesis, DMS modification assay and 1H NMR showed the presence of three guanine tetrads in the structure. Further, evidence was also found for the formation of such a G-quadruplex structure within mammalian cells. In an effort to characterize the mechanism of fragility of mcr, a unique pattern of RAG cleavage was observed in a sequence dependent manner. Three independent nicks of equal efficiency were generated by RAGs at the cryptic sequence, “CCACCTCT”, at mcr and at a cytosine upstream of it, unlike a single specific nick at the 5’ of heptamer during V(D)J rearrangement. Interestingly, RAG nicking at mcr occured in the presence of both Mg2+ and Mn2+. Using recombination assay, followed by sequencing of the junctions, we find that mcr can recombine with standard RSS in vivo, albeit at a very low frequency. Mutations to this novel motif abolish recombination at the mcr within the cells. In order to determine the prevalence of t(14;18) translocation in the healthy Indian population, nested PCR approach followed by Southern hybridization was used. Results showed 34% prevalence of t(14;18) translocation in the Indian population. Although, no gender based difference was observed, an age dependent increase was found in adults. Further, presence of the t(14;18) transcripts was also detected. The mechanism underlying the fragility of the t(10;14) translocation involving HOX11 gene in T-cell leukemia is not known. Using primer extension assays on a plasmid DNA containing HOX11 breakpoint region, presence of consistent pause sites corresponding to two G-quadruplex forming regions, flanking the patient breakpoints, were detected. These replication blocks were dependent on K+ ions. Native gel shift assays, mutation analysis, S1 nuclease and CD, further revealed formation of intermolecular G-quadruplexes, unlike the BCL2 mbr. Further, sodium bisulfite modification assay indicated the presence of such structures in the genomic DNA within cells. Hence, we propose that two independent G-quadruplex structures formed in the HOX11 gene could interact with each other, thereby resulting in fragility of the intervening sequences, where majority of the patient breakpoints are mapped. Overall, this study has attempted to understand the role of both sequence and structure of DNA, in generating chromosomal fragility during t(14;18) translocation in FL and t(10;14) translocation in T-cell leukemia. These results may facilitate future studies in unraveling the mechanism leading to genomic instability in other lymphoid cancers.