Background: Germline variants of immune-regulatory genes may affect immune checkpoint functions, disease susceptibility, disease features, and treatment response in acute myeloid leukemia. Methods: We analyzed the prevalence and potential impact of the PDCD1 gene variant rs6710479 in AML patients eligible for high-dose chemotherapy and autologous hematopoietic stem cell transplantation as consolidation treatment in first complete remission. Results: The PDCD1 rs6710479 was prevalent at elevated minor allele frequencies (MAF 0.52) in AML patients, compared to the allele frequencies reported for the European population (MAF 0.43). Baseline blood count profiles differed across PDCD1 genotypes, suggesting a link between PDCD1 rs6710479 and disease-associated levels of thrombocytopenia and leukocytosis. Conclusion: The germline PDCD1 rs6710479 variant may associate with AML disease risk and specific hematological disease features.