The human Ether-à-go-go related gene (hERG) potassium channel has been widely used to counter screen potential pharmaceuticals as a biomarker to predict clinical QT prolongation. Thus, higher throughput assays of hERG are valuable for early in vitro screening of drug candidates to minimize failure in later-stage drug development due to this potentially adverse cardiac risk. We have developed a novel method utilizing potassium fluoride to improve throughput of hERG counter screening with an automated patch clamp system, PatchXpress 7000A. In that method, ∼50% substitution of internal Cl(-) with F(-) greatly increases success rate without substantially altering the biophysical properties of the hERG channel or compromising data quality. However, effect of F(-) or other halide ions on hERG channel properties has not been studied in detail. In this study, we examined effects of complete replacement of Cl(-) in internal solution with halide ions, F(-), or Br(-). We found that (1) F(-) slightly shifts the voltage dependence of hERG channel activation to more positive voltages, while Br(-) shifts it to more negative voltages; (2) Br(-) shifts to more positive voltages both the inactivation-voltage relationship and the peak position of channel full activation of hERG; (3) F(-) slows hERG activation, while both F(-) and Br(-) make the channel close faster; (4) neither F(-) nor Br(-) have any effect on hERG inactivation kinetics. In conclusion, compared to Cl(-), F(-) has subtle effect on hERG activation, while Br(-) has distinct effects on certain, but not all biophysical properties of hERG channel.