The continuing progress in discovering lymphocyte subsets and the lengthening list of cytokines involved, together with how they are affected in primary Sjögren’s syndrome (pSS), has further fuelled the debate on pSS pathogenesis. In this review the “interferon signature” observed in the salivary glands and the role of T-cell derived cytokines (Th1/Th2 polarization, Th17 and regulatory T cells) will be discussed. A particular emphasis has been placed on the B-cell derived cytokines and especially on FLT3-Ligand, a cytokine associated with lymphoma in pSS, and B-cell activating factor (BAFF) that prevents apoptosis of autoreactive B cells. It has indeed become a challenge to understand how the interaction between several interconnected networks of cytokines impact so different cell population in the immunopathogenesis of pSS.