Starch nanocrystals (SNC), because of their interesting barrier properties, are of great interest for the formulation of biodegradable nanocomposites. Conventional production process by acid hydrolysis results in a very low yield and a heterogeneous suspension which limits the possibility of scaling up. A continuous process that includes a microfiltration step for isolating starch nanocrystals during the hydrolysis step may be a solution to increase SNC production yield. The main objectives of this study were, first, to quantify the transmission of SNC through membranes under different operating conditions and then to identify the preponderant fouling phenomenon by using simple linear fouling models. Filtration tests were run using a lab-scale microfiltration unit. It was equipped with ceramic membranes with a nominal pore sizes of 1.4 mu m and 0.8 mu m. Suspensions of nanocrystals at 0.01, 0.02 and 0.04% (w/w) were filtered in a concentration mode under different transmembrane pressures (50, 100, and 150kPa). Particle size analysis by Dynamic Light Scattering (DLS) showed that microfiltration is an effective tool for suspension fractionation. Mean diameter of SNC particles was reduced to less than 300nm in permeate. The transmission through the membrane depended on operating conditions and reached 37%. The permeate flow rate decreased with time to reach a steady value. The decrease rate was higher when the feed concentration increased. Constant pressure filtration models were used to identify the preponderant fouling phenomenon during filtration and highlighted that the decrease in permeate flow was mainly due to a cake formation on membrane surface.