Studies on cow's milk have mainly focused on analyzing specific chemical groups and natural components. Therefore, in this study, we evaluated if effect-based in vitro methods could be used as a screening tool to monitor chemical hazards in milk. In total, 32 milk samples were collected from a Swedish dairy company throughout one year. These samples included conventional and organic semi-skimmed as well as raw milk. The milk samples were tested in five in vitro methods covering eight endpoints. These endpoints included cytotoxicity, endocrine disruption (estrogen/androgen induction/inhibition), aryl hydrocarbon receptor activity, oxidative stress and DNA damage. Estrogen and androgen receptor inhibition, in addition to aryl hydrocarbon receptor activity, were the most responsive endpoints, where 10 to 13 out of the 32 milk samples were bioactive. Organic and conventional milk showed no major differences. Overall, no or only low activities were observed in milk samples in the remaining in vitro assays, which is a promising result with regard to applying effect-based methods as a screening tool. Concerning the most responsive assays, more research is needed to understand the normal background variations before they can be used as a screening tool for chemical hazards in milk.