Intrathymic injection is a common technique used for research concerning immunotolerance induction, gene therapy and T cell development in mice. Traditionally used protocols involve major surgery that exposes the thoracic cavity, which results in injury to the mice and increased risk of poor recovery and postsurgical complications such as infection. We introduce a simplified intrathymic injection technique that does not expose the thoracic cavity and virtually eliminates pain, distress and postoperative complications while maintaining high injection efficiency. The technique is suitable for both adult and neonatal mice.