Chickpea (Cicer arietinum L.), is an important legume crop in the semi-arid regions of Asia and Africa. Narrow genetic base in cultivated species made breeders efforts difficult to develop elite cultivars with durable resistance. To unravel molecular mechanisms of stress-responsive genes, expression profiling through quantitative real time-PCR (qRT-PCR) has been applied in the present study. In an earlier study, in silico expression analysis of Illumina/Solexa and Sanger sequencing data generated from drought, salinity and Helicoverpa (HVP) challenged tissues provided 2,996 abiotic and 1,451 biotic, stress-responsive genes. Of these, 53 genes for abiotic and 111for biotic tolerance were selected for experimental validation. Total RNA of root (drought and salinity) and leaf (HVP) tissues from stressed/unstressed plants were analysed in context of tolerant/sensitive genotypes. Expression profiling of 164 genes revealed significant differences in 36 including 12 novel un-annotated genes. Further analysis revealed cross talk between signaling pathways for abiotic and biotic stresses. One gene encoding for pathogenesis related (PR) protein showed differential expression in response to drought and salinity. Similarly two genes were common for drought and insect resistance (mannitol dehydrogenase, NADPH quinine oxidoreductase) and one gene (Isoflavone reductase) was common for salinity and insect resistance. Interestingly, one gene encoding for cytochrome-P450 was common to all three stresses. Majority of these stress-responsive genes are associated with ABA, ROS signaling pathways. Genetic mapping of these candidate genes, in proximity to known QTLs for tolerance to mentioned stresses may provide ‘perfect markers’ for enhancing the precision of efficiency of molecular breeding in chickpea.