Aqueous two-phase systems (ATPS) involve the combination of two immiscible polymers that at certain concentrations form a biphasic separation system. Due to the physicochemical properties and the low interfacial tension of the ATPS-forming polymers, the generation of ATPS droplets began to be explored. This work aims to characterize the generation of ATPS droplets evaluating four polyethylene glycol (PEG)-dextran (DEX) systems (combinations of molecular weights and concentrations) using Essential 8 (Gibco), DMEM-F12 (Gibco), StemLine II (Sigma-Aldrich), MSCs Basal (ATCC), RPMI 1640 (Gibco), and NutriStem (Sartorius) as ATPS solvents under in vitro conditions. In 96 well-plates, one DEX droplet of 1 μL was immersed at the bottom of the well filled with 50 μL of PEG bulk phase. ATPS droplets were generated in all tested PEG-DEX systems showing circular morphology with a mid-range diameter size in the six-culture media of 1.30 ± 0.18 mm, 1.30 ± 0.22 mm, 1.30 ± 0.43 mm, 1.21 ± 0.27 mm, 1.20 ± 0.16 mm, and 1.07 ± 0.21 mm, respectively. Uniformity was susceptible to the culture media composition showing a coefficient of variation range of 0.64–12.40 % among the four studied PEG-DEX systems. By controlling the geometry of ATPS droplets, specific cell patterns can be determined for the further construction of different cell microenvironments in 3D cultures using ATPS.