With the advent of alternative fuels, such as biodiesels and related blends, it is important to develop an understanding of their effects on inter-cycle variability which, in turn, influences engine performance as well as its emission. Using four methanol trans-esterified biomass fuels of differing carbon chain length and degree of unsaturation, this paper provides insight into the effect that alternative fuels have on intercycle variability. The experiments were conducted with a heavy-duty Cummins, turbo-charged, commonrail compression ignition engine. Combustion performance is reported in terms of the following key incylinder parameters: indicated mean effective pressure (IMEP), net heat release rate (NHRR), standard deviation of variability (StDev), coefficient of variation (CoV), peak pressure, peak pressure timing and maximum rate of pressure rise. A link is also established between the cyclic variability and oxygen ratio, which is a good indicator of stoichiometry. The results show that the fatty acid structures did not have a significant effect on injection timing, injection duration, injection pressure, StDev of IMEP, or the timing of peak motoring and combustion pressures. However, a significant effect was noted on the premixed and diffusion combustion proportions, combustion peak pressure and maximum rate of pressure rise. Additionally, the boost pressure, IMEP and combustion peak pressure were found to be directly correlated to the oxygen ratio. The emission of particles positively correlates with oxygen content in the fuel as well as in the air-fuel mixture resulting in a higher total number of particles per unit of mass. (C) 2013 Elsevier Ltd. All rights reserved.