The identification of differentially expressed genes (DEGs) is an important initial step for characterizing critical regulators and associated signaling profiles under specific conditions. Yet, a sophisticated computational tool to detect DEGs in a fully automatic manner is still lacking. Here we describe getDEG, a versatile Matlab program to fill this gap by offering efficient solutions of the most needed functions. Particularly, getDEG adopts user-designated statistical test and ranking method to prioritize probes/genes assayed. Furthermore, getDEG allows preliminary filtering by the machine detection p-value, and collapsing multiple probes to their associated gene. Taken together, getDEG is a powerful and automatic tool which satisfies basic and advanced needs in searching for most relevant candidates from microarray assays or other high-throughput screens. The tool getDEG and test examples are freely available online at https://sites.google.com/site/differentiallyexpressedgene.