The mechanism of liver damage in acute hepatitis E is poorly understood. In this study, we assessed the frequency and activation status of natural killer (NK) and natural killer T (NKT) cells and cytotoxic activity of NK cells in the peripheral blood mononuclear cells (PBMCs) obtained from patients with hepatitis E (n = 41) and healthy controls (n = 61). Flow cytometry was used to assess NK (CD3−/CD56+) and NKT cell (CD3+/CD56+) fractions (% of PBMCs) and activation status (CD69+; % of NK, NKT cells). NK cell cytotoxicity was assessed using major histocompatibilities complex-deficient K562 cells as target cells. In 14 patients, the studies were repeated during the convalescence period. Patients had fewer median (range) NK cells [8.9% (2.4–47.0) vs 11.2% (2.6–35.4)] and NKT cells [8.7% (2.8–34.1) vs 13.6% (2.3–36.9)] than controls (P < 0.05 each). Activation markers were present on large proportion of NK cells [43.5% (11.2–58.6) vs 15.5% (3.0–55.8)] and NKT cells [41.5% (17.4–71.1) vs 12.8% (3.3–63.2); P < 0.05 each] from patients. NK cell cytotoxicity was similar in patients and controls. During convalescence, all the parameters normalized. In conclusion, reversible alterations in NK and NKT cell number and activation status during acute hepatitis E suggest a role of these cells in the pathogenesis of this disease.