Nile perch Lates niloticus is an exotic predator that has had profound effects on fish communities in lakes where it has been introduced. Length-weight relationships of Nile perch in lakes Victoria, Kyoga and Nabugabo were examined to see how they had changed following the depletion of its haplochromine prey. Length-weight relationships in the new habitats were compared to those in Lake Albert and other native habitats of the Nile perch. The length to weight ratios in the new habitats were initially higher than in Lake Albert and other native habitats. After the haplochromines had been depleted, they declined to values below those of Lake Albert and most native habitats to the lowest value known. They have remained at this level for at least 15 years in Lake Kyoga, where Nile perch was introduced earliest. A similar pattern is developing in lakes Victoria and Nabugabo. Further stress on the prey population could depress the weight to length ratios to levels where it could affect the health of Nile perch stocks and make its fishery unviable. Therefore, human exploitation of Nile perch prey should be avoided. An alternative would be to heavily fish the Nile perch to increase the prey to predator ratio.