Gastric cancer is the second after lung cause of cancer-related mortality in the world. Early detection andtreatment can lead to a long survival time. Recently microarrays and next generation sequencing (NGS) havebecome very useful tools of comprehensive research into gastric cancer, facilitating the identification of treatmenttargets and personalized treatments. However, there are numerous challenges from cancer target discovery topractical clinical benefits. Although there are many biomarkers and target agents, only a minority of patientsare tested and treated accordingly. Microarray technology with maturity was established more than 10 yearsago, and has been widely used in the study of functional genomics, systems biology, and genomes in medicine.Second generation sequencing technology is more recent, but development is very fast, and it has been appliedto the genome, including sequencing and epigenetics and many aspects of functional genomics. Here we reviewinsights gained from these studies regarding the technology of microarray and NGS, how to elucidate the molecularbasis of gastric cancer and identify potential therapeutic targets, and how to analyse candidate genes. We alsodiscuss the challenges and future directions of such efforts.