The purpose of this study was to establish and automate an assay to be used for screening novel antimicrobial agents against biofilm-forming Staphylococcus aureus bacteria. The selected assay was based on crystal violet staining, which is a well used method for staining bacterial biofilms. The method was first optimised manually, antibiotic susceptibility was established and biofilm formation in plates was confirmed using atomic force microscopy. Automation of the assay was done using a Thermo Scientific Multidrop((R)) Combi dispenser and Biomek((R)) 3000 liquid handling workstation. A detailed comparison of the performance between the manual and the automated method was made in terms of screening window coefficient as well as other statistical parameters and repeatability measurements, such as plate-to-plate and day-to-day variability. Automated screening of an in-house library of natural products gave the same positive hits as previously reported, therefore the developed assay can be regarded as a reliable screening tool.