This article examines the velocity distributions of microscopic liquid-liquid two-phase flows by means of micro particle image velocimetry (micro-PIV). Aqueous droplets are dispersed into an oil bulk at the T-junction of a micro fluidic Polydimethylsiloxane (PDMS) device. The channel geometry is rectangular (H: 100μm, W: 100μm). The flow is pressure driven. Tracer particles (D: 0.5–1.2μm) are added to either phase, enabling simultaneous measurements in both phases. However, the use of immiscible liquids causes optical disturbances due to a difference in refractive indices of the two liquids and due to a curved interface geometry. Particle images are thus imaged in a distorted field of view. The results of a PIV analysis will be inaccurate in scaling as well as in location of the velocity vectors — depending on the mismatch of the refractive index. We present a basic analysis on the effect of mismatched refractive indices on the precision of the velocity measurements. The estimation is based on Snell’s law and the simplified geometry of a spherical droplet. Furthermore, we propose a method to match not only the index of refraction accurately but also to leave one additional degree of freedom to set an additional property of the liquid-liquid system, e.g. viscosity ratio or density ratio. The latter ensures that properties of the modified liquid-liquid system are close to those of the non-modified two-phase system. The findings of this study are part of the design of a Lab-on-a-Chip device. It performs a DNA analysis in an online quality control application. The miniaturization of a two-phase flow combines the benefits of confined sample compartments (i.e. droplets) with the easy-to-control process parameters of a miniaturized device (e.g. temperature, pressure). Thus band broadening of the sample by Taylor-Aris dispersion is avoided and the processes can be set accurately.