As part of a wider investigation on brain structure and function in young rats with inherited hydrocephalus, this study was undertaken to develop a technique to monitor, and quantify, progressive changes in ventricle and cortical dimensions in hydrocephalic rats in vivo. Magnetic resonance images were obtained with a T1-weighted protocol and a multislice variant of the inversion recovery sequence which displayed optimal contrast between cerebrospinal fluid and brain parenchyma. Rats were imaged at 7, 14, and 21 days after birth by taking 10 contiguous 2.0-mm coronal slices. Area and distance measurements were taken from the displayed images, enabling calculation of ventricle volumes, cortical length, and cortical thickness. The lateral ventricle volume, which was already 100-fold larger than control at 7 days, increased to over 1000 mm3 at 21 days. The anterior-posterior length of the cortex was up to 27% larger in hydrocephalics and the cortical mantle was up to 75% thinner, particularly in the posterior cortex. Subsequent fixation and histological sectioning of two 21-day-old rats showed that the smaller dimensions, which were obtained from analysis of the sections, could be accounted for by shrinkage of the tissue during dehydration and wax embedding.