This manuscript contains an assessment of tailpipe emissions and secondary aerosol formation from two in-use heavy-duty diesel vehicles (HDDVs) with different aftertreatment systems when operated with ultra-low sulfur diesel (ULSD) and hydrogenated vegetable oil (HVO) operated on a chassis dynamometer. Secondary aerosol formation was characterized from the HDDVs' diluted exhaust collected and photochemically aged in a 30 m3 mobile atmospheric chamber. Primary nitrogen oxide (NOx) and particulate matter (PM) emissions were reduced for both vehicles operating on HVO compared to ULSD. For the vehicles with no selective catalytic reduction (SCR) system, secondary aerosol production was ~2 times higher for ULSD compared to HVO. The composition of primary aerosol was exclusively organic for the vehicle with no SCR system regardless of fuel type. The composition of secondary aerosol with HVO was primarily organic for the vehicle equipped with diesel particulate filter (DPF)/SCR system; however, when the same vehicle was tested with ULSD, the composition was ~20% organic (80% ammonium nitrate). The results reported here revealed that the in-use vehicle with no-SCR had a non-functioning DPF leading to dramatic increases in secondary aerosol formation when compared to the DPF/SCR vehicle. The high-resolution mass spectra analysis showed that the POA of HVO combustion contained relatively lower portion of CH class compounds (or higher CHO class compounds) compared to ULSD under the similar conditions, which can be rationalized by the higher cetane number of HVO. Substantial growth of oxidized organic aerosol (such as m/z 44 peak) were observed after 5 h of photochemical oxidation, consistent with aged organic aerosols present in the atmosphere. The C4H9+ fragment at m/z 57 peak was used as a tracer to calculate evolution of secondary organic aerosol formation.