With the introduction of automatic milking (AM) systems, increased levels of free fatty acids (FFA) in milk were observed, which might result in off-flavours in milk and dairy products. The aim of this study was to investigate the factors contributing to elevated FFA levels: influence of the milking frequency, technical parameters of the milking system, and finally, farm management aspects. Milking frequency was studied in a Latin square design with milking intervals of 4, 8 and 12 hours and showed increased FFA-levels for the shorter intervals. Technical factors were studied in a laboratory study using milking machine components of AM-systems and conventional systems. With susceptible milk, milking machine components of AM systems showed more increased FFA levels. In some herds, FFA problems remained after solving technical and milking frequency problems. Indications were found that feed composition and feeding regime might influence susceptibility of milk for FFA-formation. These farm management aspects are subject of ongoing research.