["European Journal of Social Psychology, EarlyView. ", "\nABSTRACT\nAffective polarisation, a growing hostility toward political outgroups, is a phenomenon rooted in social identity. Social identity threat—the expectation of experiencing some form of denigration based on a self‐relevant group identity—is thought to be a major driver of affective polarisation. Using a six‐wave longitudinal survey of 470 American liberals and conservatives, we investigated the impact of social identity threat on affective polarisation, perceived stress and self‐rated health. Using random intercept cross‐lagged panel models (RI‐CLPMs), we found that higher‐than‐usual identity threat predicted subsequent increases in affective polarisation (β = 0.09, p = 0.025). There were no direct cross‐lagged effects of social identity threat on perceived stress or self‐rated health. However social identity threat was correlated at the between‐person level with stress (r = 0.25, p = < 0.001) and health (r = −0.17, p = 0.002). These findings replicate and expand on existing research by utilising a design suited for causal inference, to shed light on how identity threats and the expectation of prejudice influence intergroup relations and affective polarisation. While social identity threat plays a significant role in worsening affective polarisation, its effects on perceived stress and health are unclear. Further research is recommended to explore interventions aimed at mitigating social identity threats and polarisation, and further clarifying their potential health consequences.\n"]