Relationships between onset latency and peak-to-peak amplitude of magnetic motor evoked potentials (MMEP) after transcranial magnetic stimulation (TMS), together with the electroencephalographic parameters bispectral analysis index (BIS) and the autoregressive model with exogenous input (ARX)-derived auditory evoked potential index (AAI) were explored during different sedative and hypnotic drug combinations in six dogs. TMS was performed under sedation with acepromazine/methadone or medetomidine and after a single bolus injection of propofol or etomidate. Data for BIS and AAI were continuously collected during the periods of treatment with the hypnotic drugs. Changes in BIS and AAI during both periods were not statistically correlated with changes in onset latencies and peak-to-peak amplitudes of MMEP after TMS. Therefore, both electroencephalographic techniques are of limited use in titrating sedation and anaesthesia during TMS in the dog.