In parallel to recent progress of high-content analysis in cell biology, negative dielectrophoresis (nDEP) has continuously evolved as a potent tool for contact-free manipulation and investigation of single cells. As such, it can be especially beneficial for the handling of rare and valuable cells, e.g. in stem cell research, immunology and autologous therapy. Current nDEP applications are mainly based on flow-through systems where a small volume or single cells are pumped through microfluidic channels and analysed in seconds to minutes. Such short-term electric field exposures were repeatedly shown to be physiologically harmless. Conditions, however, might change in longer experiments when damages may accumulate. Therefore, we focus on potential limits to long-term nDEP application, with yeast serving as a model organism. Cells are reported to be successfully cultivated over several hours while suspended contact-freely in cell medium by nDEP. From comparisons of the cell division in nDEP structures under different electric conditions, conclusions are drawn with respect to which parameters govern the possible stress on the cells and how to avoid it. Firstly, the observed frequency dependence hints at an influence of the membrane polarization. Secondly, the inhibition of proliferation at high voltages is found to be overcome by external cooling of the microchips. This implies thermal effects on the cells. The warming is further examined by infrared (IR) thermometry. Despite its inherent drawbacks, IR provides a quick and easy method of determining the temperature of microfluidic systems without interfering local probes or reporter substances.