Cell culture systems are widely used for the investigation of in vitro immunomodulatory effects of medicines and natural products. Since many pharmacological relevant compounds are water-insoluble, solvents are frequently used in cell based assays. Although many reports describe the cellular effects of solvents at high concentrations, only a few relate the effects of solvents used at low concentrations. In this report we investigate the interference of three commonly used solvents: Dimethyl sulfoxide (DMSO), ethanol and β-cyclodextrin with five different cell culture systems. The effects of the solvents are investigated in relation to the cellular production of interleukin (IL)-6 or reactive oxygen species (ROS) after lipopolysaccharide (LPS) stimulation. We show that DMSO above 1 % reduces readout parameters in all cell types but more interestingly the 0.25 and 0.5 % solutions induce inhibitory effects in some cell types and stimulatory effects in others. We also found that LPS induced ROS production was more affected than the IL-6 production in the presence of ethanol. Finally we showed that β-cyclodextrin at the investigated concentrations did not have any effect on the LPS induced IL-6 production and only minor effects on the ROS production. We conclude that the effects induced by solvents even at low concentrations are highly relevant for the interpretation of immunomodulatory effects evaluated in cell assays. Furthermore, these results show the importance of keeping solvent concentrations constant in serial dilution of any compound investigated in cell based assays.