Background: Specific immunotherapy (SIT) safety has been well documented. However, the prolonged late side effects in patients who terminated SIT several years previously have been reported on in only a limited number of studies. The aim of this study was to perform a 20-year post-SIT observational evaluation for the assessment of any manifestation of serious immunological disease. Materials and Methods: In total, 1,144 patients (521 women and 623 men), with a mean age of 22.8 ± 16.9 years (at the moment of SIT completion) and who had atopic bronchial asthma and/or allergic rhinitis, were observed 20 years after immunotherapy. New neoplastic and autoimmune disease cases were monitored. The SIT group was compared to a control group consisting of 1,154 allergic patients who had never received SIT and had only had symptomatic treatment. Results: There was an inverse association between SIT treatment and the prevalence of new chronic myeloid leukemia and chronic lymphoblastic leukemia cases (OR 0.32, 95% CI 0.18-0.81 and OR 0.58, CI 0.44-0.78, respectively). In other neoplastic diseases, however, prevalences similar to those observed in the control group were confirmed. There were also no significant differences in the autoimmune disease prevalence between the analyzed groups. Conclusion: The results of this long-term observational study indicate a lack of a significant prevalence for new instances of neoplastic and autoimmune diseases, which suggests that SIT in the long term is indeed safe.