Microscale devices are promising tools to overcome specific challenges within oral drug delivery. Despite the availability of advanced high-quality imaging techniques, visualization and tracking of microscale devices in the gastrointestinal (GI) tract is still a challenge. This work explores the possibilities of applying planar X-ray imaging and computed tomography (CT) scanning for visualization and tracking of microscale devices in the GI tract of rats. Microcontainers (MCs) are an example of microscale devices that have shown great potential as an oral drug delivery system. Barium sulfate (BaSO4) loaded into the cavity of the MCs increases their overall X-ray contrast, which allows them to be easily tracked. The BaSO4-loaded MCs are quantitatively tracked throughout the entire GI tract of rats by planar X-ray imaging and visualized in 3D by CT scanning. The majority of the BaSO4-loaded MCs are observed to retain in the stomach for 0.5-2 h, enter the cecum after 3-4 h, and leave the cecum and colon 8-10 h post-administration. The imaging approaches can be adopted and used with other types of microscale devices when investigating GI behavior in, for example, preclinical trials and potential clinical studies.