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Decoding strategies manipulate the probability distribution underlying the output of a language model and can therefore affect both generation quality and its uncertainty. In this study, we investigate the impact of decoding strategies for uncertainty estimation in Large Language Models (LLMs). Our experiments show that Contrastive Search produces better uncertainty estimates across a range of alignment-tuned LLMs on average. In contrast, the benefits of these strategies sometimes diverge when the model is only post-trained with supervised fine-tuning, i.e. without explicit alignment.