Simple Summary Myelodysplastic syndromes are a group of clonal disorders originating from hematopoietic stem and progenitor cells. Due to their heterogenous nature, prognostic stratification as well as therapeutic management remain a challenge. For the majority of MDS patients, treatment strategies are risk-adapted. Current prognostic scoring systems rely on a number of key factors which help to assess the individual prognosis. Despite a number of recent advances, the integration of important patient- and disease-related parameters still falls short. This article highlights the most important scoring systems, summarizes their potential use in clinical practice, and addresses important questions on the assessment of prognosis in patients with myelodysplastic syndromes and chronic myelomonocytic leukemia. Prognostic stratification in patients with myelodysplastic syndrome (MDS) relies on a number of key factors. Combining such patient-related and disease-related prognostic parameters into useful assessment tools remains a challenge. The most widely used scoring systems include the international prognostic scoring system (IPSS), the revised IPSS (IPSS-R), the World Health Organization (WHO) Prognostic Scoring System (WPSS), and the new molecular IPSS (IPSS-M). Similar to the IPSS-R and the IPSS-M, the chronic myelomonocytic leukemia (CMML) prognostic scoring system (CPSS) and the CPSS molecular (CPSS-mol) are powerful and reliable prognostic tools that help to assess the individual prognosis of patients with CMML. The well-established prognostic assessment of MDS and CMML may be further augmented by additional disease-related parameters, such as somatic mutations, or patient-related factors, such as comorbidities. In this article, we briefly describe useful prognostic scoring systems for myelodysplastic syndromes and identify some open questions that require further investigation.