We have fabricated Si nanowire (SiNW) based ion-sensitive field effect transistors (ISFETs) for biosensing applications. The ability to prepare a large number of sensors on a wafer, the use of standard silicon microfabrication techniques resulting in cost savings, and potential high sensitivity are significant advantages in favor of nanoscale SiNW ISFETs. The SiNW ISFETs with embedded Ag/AgCl reference electrode were fabricated on a standard silicon-on-insulator wafer using electron-beam lithography and conventional semiconductor processing technology. The current-voltage characteristics show an n-type FET behavior with a relatively high on/off current ratio, reasonable sub-threshold swing value, and low gate-leakage current. The pH responses of the ISFETs with different pH solutions were characterized at room temperature which showed a clear lateral shift of the drain current vs. gate voltage curve with a change in the pH value of the solution and a sensitivity of 40 mV pH(-1). The low frequency noise characteristics were investigated to evaluate the signal to noise ratio and sensing limit of the devices.