Primary immunodeficiency disorders (PIDs) result from inborn errors in immunity. Susceptibility to infections and oftentimes severe autoimmunity pose life-threatening risks to patients with these disorders. Hematopoietic cell transplant (HCT) remains the only curative option for many. Severe combined immunodeficiency disorders (SCID) most commonly present at the time of birth and typically require emergent HCT in the first few weeks of life. HCT poses an unusual challenge for PIDs. Donor source and conditioning regimen often impact the outcome of immune reconstitution after HCT in PIDs. The use of matched or unmatched, as well as related versus unrelated donor has resulted in variable outcomes for different subsets of PIDs. Additionally, there is significant variability in the success of engraftment even for a single patient's lymphocyte subpopulations. While certain cell lines do well without a conditioning regimen, others will not reconstitute unless conditioning is used. The decision to proceed with a conditioning regimen in an already immunocompromised host is further complicated by the fact that alkylating agents should be avoided in radiosensitive PIDs. This manuscript reviews some of the unique elements of HCT in PIDs and evidence-based approaches to transplant in patients with these rare and challenging disorders.