Malignant bone tumors (MBT) are a rare and heterogeneous group of tumors, arising mostly in children. Localized disease is usually treated with surgery, but prognosis worsens in advanced stages. Currently, with limited biomarkers in clinical use, prognosis depends on histological grading and clinical features. However, the use of biomarkers remains inadequate, limiting treatment efficacy and increasing the risk of recurrence and disease progression for patients. Potential biomarkers based on genomics, proteomics, and clinical characteristics are currently entering clinical use in multiple cancers. Biomarker research in MBT faces additional challenges resulting from the rarity of these entities. Emerging biomarker concepts require clinical validation to create robust frameworks for precision oncology. This review of new biomarkers is based on relevant literature from Pubmed, Scopus, and clinicatrials.gov databases retrieved in November 2023. At present, the definition of prognostic markers in malignant bone tumors remains challenging. More research is needed, particularly to tailor treatments based on advanced genetic profiling and analysis of individual tumor and patient characteristics. Many newly identified biomarkers have not been clinically validated.