Amplitude modulation of the eyeblink component of the startle response is a commonly used index for the emotional state of an organism. The use of electromyography (EMG) to determine startle eyeblink amplitudes during functional magnetic resonance imaging (fMRI) is limited as interactions between strong switching magnetic fields, radio pulses and electrodes introduce large artefacts in EMG recordings. We demonstrate a robust linear correlation between time courses and amplitudes of startle eyeblinks recorded by EMG and infrared oculography (IOG), an fMRI compatible technique based on infrared light reflection from the subject's eye. Moreover, our data indicate that IOG, like EMG, recordings of startle eyeblink amplitudes are predicted by verbal ratings of the emotional valence of pictorial foreground stimuli. Thus, IOG provides a valid method to record startle eyeblinks and might be used to monitor affective state during fMRI.