We used a digital stereo-video camera system for three-dimensional monitoring of cultured Pacific bluefin tuna, Thunnus orientalis, swimming freely in a net cage. We estimated the fork length and length frequency distribution of individual fish using the direct linear transformation (DLT) method. Information obtained from stereo images is useful for managing the growth of tuna during rearing. Our aim was to develop a simple method involving a combination of DLT and commercial image-processing software to enable aquaculturists to obtain three-dimensional measurements of fish. In this study, we used a stereo-video camera system to evaluate the precision and validity of fish size estimates determined from repeated measurements. Of the total assessed individuals swimming within a distance of <5.5 m from the camera system, estimates for 99% (106/107) were found to be valid, with an error ratio (standard error/mean) of <5%. Therefore, we believe that our proposed simple method for monitoring free-swimming fish could be very useful for aquaculture management.