In this article, we would like to present rare diseases, which are immunodeficiency, centromeric instability and facial dysmorphism syndrome (ICF), and myelodysplastic neoplasm (MDS), with possible complications of their course and treatment with particular emphasis on pulmonary alveolar proteinosis (PAP). We are basing that review on our experience that we have gained through the diagnostic and treatment process of our pediatric patient. MDS is a rare disease among children that has a different and uncharacteristic clinical course and genetic background in comparison to MDS occurring in adults. Regarding the uncharacteristic clinical picture, the differential diagnosis can be a challenge for clinicians. In that process also diseases characterized by immunodeficiency should be taken into account, including the ICF. ICF type 2 is an autosomal recessive disease that manifests by agammaglobulinemia or hypogammaglobulinemia, developmental delay, and facial anomalies. Both ICF and MDS can be treated with an allogeneic hematopoietic stem cell transplantation. One of the possible complications in the course and treatment of MDS and ICF can be PAP. Its pathogenesis is based on the accumulation of surfactant in alveoli that leads to pulmonary insufficiency. As hematologic diseases and their treatment are known for their impact on multiple systems, we find the unique value of this article in being the first description of the coexistence of ICF type 2 with PAP.