Natural killer (NK) T lymphocytes are thought to act as regulatory cells directing early events during immune responses. Murine NKT cells express inhibitory receptors of the Ly49 family. These receptors have a well-established and crucial role in modulating NK cell activities, but their physiological role in regulating NKT cells is not well understood, nor is the influence of major histocompatibility (MHC) ligands on endogenous Ly49 expression. We have further investigated how the expression of inhibitory NK receptors is regulated on NKT cells, and demonstrate a non-random expression of ligated Ly49 molecules on CD1d-restricted NKT cells. The nature of the T-cell receptor on the NKT cell crucially determines the profile of expressed Ly49 isoforms. Further, we show that MHC class I ligands efficiently modulate the expression levels of the inhibitory receptors, and the frequencies of cells positive for the Ly49 members. In addition, we find a several-fold increase in Ly49C/I-expressing NKT cells in adult thymus, apparently independent of MHC class I molecules. Abundant expression of Ly49 receptors on NKT cells, and the striking differences found in Ly49 isoform patterns on NKT-cell subsets differing in T-cell receptor expression, suggest that the pattern of Ly49 expression is tuned to fit the T-cell receptor and to emphasize further a role for these receptors in NKT immunity.