<jats:title>Abstract</jats:title><jats:p>Magnetic resonance imaging (MRI) was applied to determine the sex of polar cod (<jats:styled-content style="fixed-case"><jats:italic>Boreogadus saida</jats:italic></jats:styled-content> Lepechin, 1774) (Actinopterygii: Gadidae) and to follow the gonadal development in individual animals over time. Individual unanaesthetised fish were transferred to a measurement chamber inside a preclinical 9.4 T MRI scanner and continuously perfused with aerated seawater. A screening procedure at an average of 3.5 h, consisting of a set of MRI scans of different orientations, was repeated every 4 weeks on the same set of reproducing <jats:styled-content style="fixed-case"><jats:italic>B. saida</jats:italic></jats:styled-content> (<jats:italic>n</jats:italic> = 10) with a body length of about 20 cm. Adapted multi‐slice flow‐compensated fast low‐angle shot (FcFLASH) and rapid acquisition with relaxation enhancement (RARE) protocols with an in‐plane resolution of 313 μm and an acquisition time of 2.5 min were used to visualise the morphology of various organs, including the gonads within the field of view (FOV). The MR images provided high resolution, enabling specific sex determination, calculation of gonad volumes, and determination of oocyte sizes. Gonad maturation was followed over 4 months from November 2021 until shortly before spawning in February 2022. The gonad volume increased by 2.3–25.5% for males and by 11.5–760.7% for females during the observation period. From October to February, the oocyte diameter increased from 427 μm (<jats:italic>n</jats:italic> = 1) to 1346 ± 27 μm (<jats:italic>n</jats:italic> = 4). Interestingly, individual oocytes showed changes in MR contrast over time that can be attributed to the morphological development of the oocytes. The results fit well with previous literature data from classical invasive studies. The presented approach has great potential for various ecophysiological applications such as monitoring natural or delayed development of internal organs or sex determination under different environmental conditions.</jats:p>