Herein we investigated how rituximab-induced B cell depletion affected leukocyte subpopulations and antibody titers in SLE patients. We focused our analysis on time points related to absence and return of B cells after depletion. A correlation was found between the baseline frequency and time to repopulation; the fewer B cells initially, the longer to their return. While the few B cells remaining after treatment were of memory, double-negative (IgD-CD27-), and CD5+ phenotype, the returning B cells were mainly naïve, indicating de novo production of B cells. Serum levels of IgG and antibodies against Ro52, Ro60, La44, measles and tetanus remained unchanged, while decreases in IgM, IgE, anti-dsDNA and anti-C1q antibodies were observed. Additionally, a significant increase in activated CD4+ and CD8+ T cells, as well as CD25bright FOXP3+ regulatory T cells was observed. In conclusion, both the humoral and the cellular immune systems were affected by treatment with rituximab.