Exposure to immunosuppressive medication in utero is an important cause of secondary T cell lymphopenia in infancy, which can be detected via T cell receptor excision circle (TREC) quantification on severe combined immunodeficiency (SCID) newborn screening (NBS). At present, there is a paucity of literature surrounding management of these infants. A protocol including recommendations for vaccinations and follow-up is needed to augment care. Patients referred to immunology for abnormal TREC results on NBS were identified as having in utero exposure to immunosuppressive medications and were followed until lymphopenia improved. The natural history of these patients' lymphopenia was used to develop general management guidelines. Four infants with low TRECs secondary to in utero immunosuppressive exposure were evaluated. Medication exposures included azathioprine, infliximab, hydroxychloroquine, and fingolimod. All infants were born full term. TRECs ranged from 101-206 (normal value in IL ≥ 250 at time of testing, B-actin control). T cell lymphopenia (CD3 &lt; 1500) was present in 50% of cases. Undetectably low effector CD4 naïve T cell population was present in 100% of cases. Mitogen proliferation was uniformly normal. Severity of TREC abnormality did not correlate with presence of T cell lymphopenia. Immune abnormalities normalized in 75% patients by age 4 months. All age-appropriate vaccinations, including live vaccines, were administered to all patients by age 4 months. It is critical to assess for in utero immunosuppressive exposure in infants with abnormal TREC results on NBS. In the infants evaluated, secondary T cell lymphopenia associated with maternal immunosuppressive use resolved or significantly improved by age 4 months. Once abnormal TREC count is deemed to be secondary to in utero immunosuppression and there are no other contraindications, infants may safely receive live vaccination, are able to drink breast milk, and do not require prophylactic anti-microbials.