The print quality of prints performed with flexographic printing technology is influenced by various parameters such as viscosity of the printing inks, printing substrates, plates, anilox rolls, etc. The aim of this work is to analyze the influence of ink viscosity, printing plate and printing base on selected properties of print quality, such as optical density of full tone area and the increase of tonal value (TVI). Additionally, the printed dots on 5, 15, 30, 50 and 75% of half tone area were investigated using digital microscopy. The least square fitting method in a matrix form was successfully used in order to confirm the influence of printing process parameters on print quality. The results obtained reveal the significant influence of the printing plate and printing substrate characteristics and the lesser influence of printing ink viscosity for 40–100% coverage area. The values of the optical densities of full tone areas are mainly influenced by the properties of the printing plate and the printing base. Furthermore, the optical density decreases when the value of flow time decreases, which is related to the lower thickness of dried ink film. The TVI on light tones (0 to 20%) is mainly influenced by the ink viscosity.