This systematic review examines the application of Deep Learning (DL) in genomics and histopathology for precision oncology. The study, covering publications from 2010 to November 2023, identified 534 relevant articles, categorized into basic (diagnosis, grading, subtyping) and advanced (mutation, drug response, survival prediction) applications. The analysis reveals that DL is predominantly used in histopathology, with a notable surge in both basic and advanced applications. In contrast, genomics applications are more focused on pan-cancer contexts and advanced tasks like mutation prediction and drug response. Multimodal DL, which integrates both histopathological images and genomic data, is a niche topic with limited publications, primarily focusing on prognosis predictions. The review highlights the potential of multimodal DL in advanced tasks and the need for further research to bridge existing gaps in these fields. Despite the challenges, the integration of DL in histopathology and genomics shows significant promise in advancing precision oncology.This systematic review examines the application of Deep Learning (DL) in genomics and histopathology for precision oncology. The study, covering publications from 2010 to November 2023, identified 534 relevant articles, categorized into basic (diagnosis, grading, subtyping) and advanced (mutation, drug response, survival prediction) applications. The analysis reveals that DL is predominantly used in histopathology, with a notable surge in both basic and advanced applications. In contrast, genomics applications are more focused on pan-cancer contexts and advanced tasks like mutation prediction and drug response. Multimodal DL, which integrates both histopathological images and genomic data, is a niche topic with limited publications, primarily focusing on prognosis predictions. The review highlights the potential of multimodal DL in advanced tasks and the need for further research to bridge existing gaps in these fields. Despite the challenges, the integration of DL in histopathology and genomics shows significant promise in advancing precision oncology.