The remarkable performance of large language models (LLMs) in generation tasks has enabled practitioners to leverage publicly available models to power custom applications, such as chatbots and virtual assistants. However, the data used to train or fine-tune these LLMs is often undisclosed, allowing an attacker to compromise the data and inject backdoors into the models. In this paper, we develop a novel inference time defense, named CleanGen, to mitigate backdoor attacks for generation tasks in LLMs. CleanGen is a lightweight and effective decoding strategy that is compatible with the state-of-the-art (SOTA) LLMs. Our insight behind CleanGen is that compared to other LLMs, backdoored LLMs assign significantly higher probabilities to tokens representing the attacker-desired contents. These discrepancies in token probabilities enable CleanGen to identify suspicious tokens favored by the attacker and replace them with tokens generated by another LLM that is not compromised by the same attacker, thereby avoiding generation of attacker-desired content. We evaluate CleanGen against five SOTA backdoor attacks. Our results show that CleanGen achieves lower attack success rates (ASR) compared to five SOTA baseline defenses for all five backdoor attacks. Moreover, LLMs deploying CleanGen maintain helpfulness in their responses when serving benign user queries with minimal added computational overhead.