Binary information is prevalent in the environment. In this study, we examined how people process repetition and alternation in binary sequences. Across four paradigms involving estimation, working memory, change detection, and visual search, we found that the number of alternations is under-estimated compared to repetitions (Experiment 1). Moreover, recall for binary sequences deteriorates as the sequence alternates more (Experiment 2). Changes in bits are also harder to detect as the sequence alternates more (Experiment 3). Finally, visual targets superimposed on bits of a binary sequence take longer to process as alternation increases (Experiment 4). Overall, our results indicate that compared to repetition, alternation in a binary sequence is less salient in the sense of requiring more attention for successful encoding. The current study thus reveals the cognitive constraints in the representation of alternation and provides a new explanation for the over-alternation bias in randomness perception.