Plants are exposed to various abiotic stresses such as water deficit or ion excess, elevated temperature, high light intensity, salinity, freezing, cold, etc. under field conditions, potentially reducing the yield of crop plants by more than 50%. Investigations of the physiological, biochemical and molecular aspects of stress tolerance have been conducted to unravel the intrinsic mechanisms for mitigation against stress. The new molecular “omic” tools, comprising of genomics, proteomics and metabolomics, have opened up new perspectives in stress biology. Before the advent of genomics era, a gene-by-gene approach was used to decipher the function of genes involved in abiotic stress response. The availability of genome sequences of certain important plant species has enabled the use of strategies like genome-wide expression profiling to identify the genes associated with stress response, followed by the verification of gene function by the analysis of mutants and transgenics. The genomics based approaches provide access to agronomically desirable alleles present at quantitative trait loci (QTLs), thus enabling the improvement of abiotic stress tolerant plants. Marker assisted selection (MAS) is already helping breeders improve drought related traits. The recent upsurge in structural genomics determines the DNA sequence by manual or robotic methods. Further elucidation of the complex networks interacting during stress defenses has been achieved by multi-parallel analysis of transcript levels, microarray analysis, RT-qPCR, Serial analysis of gene expression (SAGE), Massive parallel signature sequencing (MPSS) and more recently oligoarray using the transcriptome of any specie to evaluate abiotic stress response. Analysis of sequence data and gene products would facilitate the identification and cloning of genes at target QTLs and their direct manipulation via genetic engineering. Furthermore, several bioinformatic tools, ESTs and subtractive cDNA libraries have added new dimensions for deciphering the genetic basis of stress tolerance. The current initiatives in functional genomics or proteomic research for the analysis of plant stress tolerance is based on two-dimensional gel electrophoresis (2-DE) and identification of differentially displayed spots by MALDITOF, QTOF MS/MS, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), characterization of separated proteins by mass spectrometer and database searching. In addition, many proteins are modified by post-translational modifications such as phosphorylation, glucosylation, ubiquitinylation, sumoylation and many others. New techniques in gel-based approaches such as difference gel electrophoresis (DIGE) can provide both qualitative and quantitative data about the differential expression of proteins. Proteomics nowadays is also used to study the relationship between gene expression (transcriptomics) and metabolism (metabolomics). Our limited knowledge of stress-associated metabolism remains a major gap in our understanding of the stress response. Therefore comprehensive profiling of stress-associated metabolites is most relevant to the successful molecular breeding of stress-tolerant crop plants. Metabolomic studies, thus along with transcriptomics and proteomics, and their integration with systems biology, will lead to strategies to alter cellular metabolism for adaptation to abiotic stress conditions. The present review will focus on the current development, progress and applications of genomics, proteomics and metabolomic studies, and implementation of systems biology to meet the challenges of abiotic stress and crop improvement program from a practical standpoint. The accumulating information will provide plant researchers to explore new paradigms to address fundamental and practical questions in a multidisciplinary manner.