We investigated whether extremely geomagnetic activity may modify the association between short-term nitrogen dioxide (NO₂) exposure and emergency hospitalization for acute coronary syndrome (ACS). A case-crossover study design was used to analyze ACS in 6,594 hospitalized patients at the Clinic of Kaunas, Lithuania. We evaluated the associations between NO₂, geomagnetic activity and the rate of emergency admissions for ACS by logistic regression controlling for seasonal variation, weekdays and meteorological factors. Ambient NO₂ pollution interquartile range increase (IQR) on the day of admission and previous day (lag 0-1) in patients below 65 years of age increase the risk of ACS equal to 24% (95% CI 0.96-1.60). Evidence of effect modification by combined NO₂ and geomagnetic activity was observed in relation to ACS, adjusted OR was 1.61; 95% CI 1.03-2.53. In conclusion, these findings suggest that geomagnetic activity variations may increase the traffic-related air pollution effect on ACS, and highlight environmental factors associated with ischemic heart disease course.