A microchip processing apparatus, comprising a holding part for holding a microchip having channels including a main separation channel in which analysis is performed while a solution moves inside a plate-like member, a separation buffer solution filling device for filling separation buffer solution into said microchip, a sample injection device for injecting a sample into said microchip, a power supply device for applying electrophoresis voltage to said main channel, and a control part for controlling filling of separation buffer solution into said channel, introduction of samples, and electrophoretic separation, wherein it is characterized in that:
- said control part includes also a function by which, after filling separation buffer solution into said channel and before injecting the sample into the channel, a voltage is applied to said channel by said power supply device and an electrified state at that time is monitored, and it is determined from that electrified state as to whether the filling of the buffer solution is normal or not.