Relatively little is known about the influence of sex and the circadian rhythm on gastrointestinal transit. However, these factors could have an important impact on aspects such as digestion, oral absorption of drugs or the clinical manifestation of gastrointestinal diseases, among others. Remarkably, preclinical models have scarcely taken these factors into consideration. In this study, we assessed the gastrointestinal transit of young adult Wistar Han rats of both sexes, under normal and inverted light cycle. To do this, serial radiographs were taken for 24 h (T0–T24) after intragastric barium administration and subsequently analysed to construct transit curves for each gastrointestinal region. Under a normal light cycle, transit curves were similar, except for a slower transit in females compared with males from T8 to T24. Under the inverted cycle, there was a significant acceleration in stomach emptying (similar in both sexes), emptying of the small intestine (even faster in females) and filling of the caecum and colon (which was also even faster in females). This study confirms, using X-ray non-invasive methods for the first time, that both sex and circadian rhythm (probably through its effect on behaviour) influence gastrointestinal transit in laboratory animals.