Low-risk patients with myelodysplastic syndromes (MDS) are inclined to long-term accumulation of iron in the organs due mostly to red blood cell transfusion and ineffective erythropoiesis. The effect of free toxic iron species in the liver and heart sites is well known, but recent knowledge assumes that oxidant-mediated tissue injury is also effective in the bone marrow. We aimed to investigate the predictive value of bone marrow iron accumulation as demonstrated by Perls staining on the overall survival (OS) of MDS patients. We retrospectively analyzed 114 low and intermediate-I IPSS risk MDS patients who were diagnosed at our institution in the last 20 years. The median age was 70 years (range 32–93). Two different experienced hematologists analyzed all samples. Perls Prussian blue stain was used to stain the bone marrow, which was assessed by modified Gale’s grading and then correlated with the outcome. Twenty-seven patients had grade 1 (+), 31 grade 2 (++), and 56 grade 3 (+++). The 20-year OS was significantly lower in patients with a higher Perls score (6.8 ± 6.1%, median 80 ± 7 months in grade 3; 18.7 ± 9.4%, median 70 ± 17 months in grade 2; 33.2 ± 16.4%, median 144 ± 18 months in grade 1; p = 0.011); bone marrow iron overload (p = 0.003; HR 1.7) and transfusion dependency (0.001; HR 2.6) negatively impacted on survival. We suggest that a higher grade of iron storage at diagnosis can impact on the outcome in MDS patients. Perls stain, together with ferritin and the blood transfusional burden, could be another marker at diagnosis of iron-related toxicity that predicts survival.