PatchXpress, an automated 16-channel parallel patch clamp system, was used to determine inhibition of human ether-a-go-go related gene (hERG) potassium channels by known blockers. A monoclonal cell line stably expressing hERG potassium channels was generated in CHO-KI cells. Results were compared to conventional patch clamp experiments using similar voltage protocols and solutions. Success rates were evaluated for cell recordings under a variety of conditions, including Accumax versus trypsin treatment to harvest cells, single versus double compound additions, and polystyrene versus glass-coated compound plates. We found that the average success rates rose from 27% with trypsin treatment to 38% with Accumax treatment, which improved to 55–65% following long-term culturing using only Accumax to harvest cells. Two drug additions (spaced 1 min apart with suction off) were also found to produce data that more closely matched conventional experiments. Finally, polystyrene versus glass-coated compound plates were evaluated, and we found that for some compounds (but not all), preparation of compound samples in glass-coated plates resulted in inhibition that more closely matched data obtained by conventional experiments. Therefore, we have established an assay to evaluate the ability of compounds to inhibit hERG potassium channels, which closely matches data produced using conventional methods but with much greater throughput.