Objective To determine the effect of a fish protein isolate (FPi), administered over 6 months, on the growth of children aged 6-36 months, measured by Z-scores of height-for-age (HAZ) and weight-for-height (WHZ), compared with the standard meal without FPi; and to determine the safety and acceptability of FPi daily consumption. Design Cluster-randomized community-based controlled trial. For 6 months, the centres received either FPi replacing 50 % of total proteins in the diet or standard protein. HAZ and WHZ were used to determine the effect on growth. Acceptability was determined by daily consumption, measured by weighing the servings before and after consumption. Setting Day care centres and community nutritional centres in northern Lima, Peru. Subjects Children (n 441) aged 6-36 months. Results Four centres were randomized to the intervention with FPi, five centres were randomized to the standard control diet. More than 36 900 meals were prepared and administered in a supervised manner. Both groups received the same amounts of energy and proteins daily (proteins about 12-15 % of total energy). Growth of children who received the FPi diet was similar to that of children with the standard diet. Consumption was similar in the FPi and control groups (70 v. 80 % of amount offered, respectively). The protein was safe and well tolerated. No adverse events were reported. However, the cost of the intervention with FPi was 20-40 % lower v. the standard diet with animal protein derived from beef, chicken, eggs or liver. Conclusions The FPi was well accepted and there was no significant difference in growth between both groups. FPi is a potential source of animal protein at lower cost.