Pollutants are a major issue of diesel engines, with oxides of nitrogen (NOx) and airborne total particulate matter (TPM) of primary concern. Current emission standards rely on laboratory testing using an engine dynamometer with a standard test procedure. Results are reported as an integrated value for emissions from a transient set of engine speed and load conditions over a length of time or a set of prescribed speed-load points. To be considered a valid test by the US EPA, the measured engine speed and load are compared to the prescribed engine speed and load and must be within prescribed regression limits. To explore differences in NOx, TPM, carbon monoxide (CO), total hydrocarbons (THC), and fuel consumption based on the control algorithm used to set the engine speed and load, five diesel engines (1991 DDC S60, 1992 DDC S60, 1999 Cummins ISM, and 2004 Cummins ISM) were operated on the heavy-duty transient FTP cycle with two different engine control settings and a second 1992 DDC S60 incorporated three different engine control settings. From the least to the most aggressive accelerator pedal position control (APPC) studied, the brake-specific emissions of THC, CO, NOx, and TPM were found to differ up to 14.0%, 33.9%, 2.4%, and 19.6%, respectively. The older engine technology were influenced the most while the 2004 Cummins ISM was influenced the least by the control algorithm due to improved engine control with the variable geometry turbocharger (VGT) reducing turbocharger lag, which causes relatively rich zones inside the cylinder. A wider range of APPC aggressiveness than tested would still produce valid transient tests and cause variation between test facilities; therefore, tighter regression tolerances are suggested.