The effects of combining premixed, low temperature combustion (LTC) with biodiesel are relatively unknown to this point. This mode allows simultaneously low soot and NOx emissions by using high rates of EGR and increasing ignition delay. This paper compares engine performance and emissions of neat, soy-based methyl ester biodiesel (B100), B20, B50, pure ultra low sulfur diesel (ULSD) and a Swedish, low aromatic diesel in a multi-cylinder diesel engine operating in a late-injection premixed LTC mode. Using heat release analysis, the progression of LTC combustion was explored by comparing fuel mass fraction burned. B100 had a comparatively long ignition delay compared with Swedish diesel when measured by start of ignition (SOI) to 10% fuel mass fraction burned (CA10). Differences were not as apparent when measured by SOI to start of combustion (SOC) even though their cetane numbers are comparable. Overall, cetane number was a better indicator of combustion phasing as measured by start of injection to 50% mass fraction burned (CA50) than ignition delay when comparing biodiesel with petroleum diesel in premixed LTC. To normalize for combustion phasing, injection timing was adjusted to achieve the same CA50 point for a baseline condition with each fuel. NOX emissions were the same among fuels for a given CA50 whether combustion phasing was adjusted by changing injection timing or injection pressure. Hydrocarbon (HC) emissions for B100 were lower than for ULSD and the same as for Swedish diesel. The filter smoke number (FSN) decreased as the concentration of biodiesel was increased although the particle size distribution increased indicating higher levels of soluble hydrocarbon species were present.