This study investigates the emission characteristics of toxic organic pollutants (PAHs, PCDD/Fs, and PCBs) generated by a heavy-duty diesel engine operating at various exhaust gas recirculation (EGR) rates during steady-state cycles. Tests on the exhaust gas composition were conducted before and after changing the EGR ratio. The fuel used in the study (B2 diesel) was a mixture of 2% biodiesel and 98% diesel. The main focus was on the emission factors for the organic toxic pollutants in the exhaust gas after EGR ratios of 0% and 5% were applied. At an EGR ratio of 5%, the total mass emission factors for the PAHs and PCBs increased by 3.87 times and 14.2 times, respectively, while the toxic equivalency factors increased by 2.65 times and 5.01 times, respectively. A significant increase in pollutants with a higher molecular weight, particularly for the PAHs, was observed after applying an EGR ratio of 5%, implying incomplete combustion. The concentrations of carbon dioxide (CO2) and nitric oxides (NOx) decreased by 2.5% and a 54.4%, respectively, when the EGR ratio was increased from 0% to 5%, but the concentrations of PM2.5 and carbon monoxide (CO) increased by 60.5% and 66%, respectively. Therefore, a combination of control strategies is necessary in order to achieve a significant reduction in the emission of all pollutants.