This manuscript describes the importance of using histological methods to assess the effects of feed on the liver and intestine of fish. Due to the constantly increasing world production of fish and other aquatic organisms, it is necessary to replace fishmeal and fish oil in diets with less expensive raw materials of plant origin. Due to the increased fiber content, increased presence of carbohydrates, antinutritional factors, and inappropriate content of amino acids and new compounds can have negative effects on the digestive system of fish and therefore on fitness, health  and production characteristics of cultivated fish. The liver and intestines are the most important organs for the digestion and absorption of nutrients from feed. Therefore, monitoring histological structure of fish liver and intestine is the method of choice in assessing the effects of nutrient mixtures that use raw materials of plant origin. For both of these vital organs the normal histological structure and the most important results obtained by research are discussed. This paper presents a critical review of the histological methods used in research on feed effects. Results related to the negative effects of raw soy-based feed on the occurrence of enteritis in carnivorous fish species are discussed. The results point out that use of modern approach in fish pathology such as improved histochemical, stereological, scoring, and other analytical methods could be a beneficial approach in an accurate assessment of new feed effects on fish.