Background and objectives: Despite global warming, the climate in Northern Europe is generally cold, and the large number of deaths due to non-optimal temperatures is likely due to cold temperatures. The aim of the current study is to investigate the association between cold temperatures and all-cause mortality, as well as cause-specific mortality, in Tallinn and Riga in North-Eastern Europe. Materials and Methods: We used daily information on deaths from state death registries and minimum temperatures from November to March over the period 1997–2015 in Tallinn and 2009–2015 in Riga. The relationship between the daily minimum temperature and mortality was investigated using the Poisson regression, combined with a distributed lag non-linear model considering lag times of up to 21 days. Results: We found significantly higher all-cause mortality owing to cold temperatures both in Tallinn (Relative Risk (RR) = 1.28, 95% Confidence Interval (CI) 1.01–1.62) and in Riga (RR = 1.41, 95% CI 1.11–1.79). In addition, significantly increased mortality due to cold temperatures was observed in the 75+ age group (RR = 1.64, 95% CI 1.17–2.31) and in cardiovascular mortality (RR = 1.83, 95% CI 1.31–2.55) in Tallinn and in the under 75 age group in Riga (RR = 1.58, 95% CI 1.12–2.22). In this study, we found no statistically significant relationship between mortality due to respiratory or external causes and cold days. The cold-related attributable fraction (AF) was 7.4% (95% CI -3.7–17.5) in Tallinn and 8.3% (95% CI -0.5–16.3) in Riga. This indicates that a relatively large proportion of deaths in cold periods can be related to cold in North-Eastern Europe, where winters are relatively harsh.