Although long thought of as “gene relics,” pseudogenes have recently gained research and medical interests because of their potential impacts on cellular pathways and of their clinical relevance. Studies have profiled pseudogenes at both DNA and RNA levels in cancers. Differences in pseudogene expression (RNA) or occurrence (DNA) help cancer subtype classification, which in turn can contribute to improving treatment selection in precision medicine. Such differences are also associated with clinical outcomes, such as patient survival. Here we review the existing methods on pseudogene profiling and discuss the application scenarios, as well as their relevant issues and challenges.