We are interested in monitoring an individual’s emotions during the reading of a novel. While physiological responses to experimentally induced emotions are often small and inconsistent, being engaged in a novel may elicit relatively strong responses. We analyzed EEG, ECG, skin conductance and respiration of 57 readers reading a complete, yet to be published novel written by a popular contemporary writer (Arnon Grunberg) and compared physiology during the reading of pre-defined sections that were either emotionally intense or not. Heart rate was lower while reading emotional sections. We also found effects of emotional intensity on breathing variability and alpha asymmetry. Most of the examined physiological variables were strongly affected by time on task. We could estimate whether the physiological data of an individual reader were collected during the reading of an emotional or non-emotional section with an accuracy of up to 72% using individualized models and after correcting data for individually modeled time-related effects. Our results imply that using our methodology, it is possible to examine fluctuating reader’s emotion during the reading of a novel after reading, but not (yet) in real time.