We discuss the combination of a CARS-imaging system with microfluidics. Such system is a versatile tool to quantify the relative contributions of resonant and non-resonant scattering at the CARS frequency. We will show that the two-channel microfluidic chip employed in combination with deuterated isotopomers as an internal standard allows for fast and quantitative detection of organic molecules by CARS microscopy. The experimental design enables the simultaneous measurement of both the chemically relevant Raman-resonant signal and the non-Raman-resonant background.