The immune recovery (IR) following the allogeneic hematopoietic stem cell transplantation (allo-HSCT) is an advancement procedure that fundamentally correlated to the curative success. It is critical to understand the interfering factors in IR to prevent the HSCT-related mortality. The factors influencing CD4+T cell recovery post (HSCT) are not well totally characterized. This work was conducted to analyze the kinetics of CD4+T cell subsets recovery post HSCT, and to correlate their reconstitution with different factors that may influence the overall survival following HSCT. We prospectively evaluated the clinical outcomes and CD4+ T lymphocyte subtypes regeneration kinetics at different time-points of 22 patients with allogeneic HSCT for malignant and non-malignant diseases from 2007 to 2008. Statistics (means, minimal, and maximal values) were used to describe patient baseline characteristics. Results were presented as absolute count of CD4+ T cells, % of naive and memory subsets, and p-values. Thymus-independent pathways were responsible for the rapid recovery of memory CD4+T cells less than 6 months after HSCT. Thymus-dependent pathways were activated between 6 and 12 months in the majority of patients with increasing counts of naive CD4+ T cell. Furthermore, increasing patient age and chronic GVHD predicted the slow naive T cell recovery and also predicted high memory T cell numbers. The proper CD4 + reconstitution was associated with younger age, a non-malignant disease and a lower incidence of acute graft-versus-host disease ≥ grade 2. Additionally, the CD4+ T lymphocytes recovery ≥ 200/µl was associated with a higher overall survival. Different factors affected the IR post the allo-HSCT. The CD4+ count ≥ 200/µl was a simple IR predictor of overall survival and better clinical outcome following allogeneic HSCT.