The aim of this study was to evaluate which factors determined immediate mortality of Common Tern (Sterna hirundo) chicks during a heavy rainfall. On 26 June 2013, a heavy rainfall event was recorded at an inland colony of Common Terns in central Poland that resulted in the death of ~30% of the chicks. The highest mortality rate was recorded in the youngest age group (1–8 days). Probability of surviving the rainfall increased 1.47 (95% CI: 1.25–1.83) times with each additional day. There was also a positive relationship between survival probability and mass-size residuals of chicks (β = 0.17 ± 0.07, P = 0.025). This study provides evidence for age-and condition-dependent mortality of semi-precocial chicks during an extreme weather event.