Background: Immune reconstitution (IR) after allogenic hematopoietic stem cell transplantation (allo-HSCT) is a long and progressive process intrinsically correlated to therapeutic success. It is essential to understand interfering factors in IR to prevent HSCT-related mortality. Methods: We retrospectively evaluated absolute lymphocyte count (ALC) and lymphocyte subtypes of 111 pediatric patients with allogeneic HSCT for malignant and non-malignant diseases from 2013 to 2018. ALC recovery on day +30 (D+30), +100 (D+100) and +180 (D+180) and subtypes CD3+CD4+, CD3+CD8+, CD19+ and CD16+CD56+ on D+100 were correlated to the HSCT procedure, clinical outcomes, and survival. Results: ALC had a gradual increase on D+30, D+100 and D+180 (medians 634/μL, 1 022/μL and 1 541/μL, respectively). On D+100, CD3+CD8+ achieved the highest recovery rate (68%), followed by CD16+CD56+ (47%), CD3+CD4+ (39%) and CD19+ (8%). Adequate ALC recovery on D+30 was associated with age <8 years, bone marrow grafts, myeloablative conditioning, and non-haploidentical donors. The use of serotherapy correlated to a poor ALC recovery on D+180. Counts of ALC and CD3+CD8+ on D+100 were higher in patients with cytomegalovirus infection. CD3+CD4+ recovery was associated with age <8 years, non-malignant disease and a lower incidence of acute graft-versus-host disease ≥grade 2. Further, ALC and CD3+CD4+ recovery on D+100 resulted in higher overall survival, as ALC was determinant regardless of disease type (HR 3.65, 1.05-12.71, P=0.04). Conclusion: Several factors influenced IR after allo-HSCT. ALC≥500/μL on D+100 was found to be a simple IR biomarker and a good predictor of survival, easily available to resource-limited countries.