The structure of the hull of the project 1288 trawler in a region of fore hold was improved to ensure fatigue strength of assemblies of the intersection of main frames with the second bottom. To this end, a study of the fatigue strength of these assemblies was carried out for the original side structure and two versions of its modernization. Values of internal forces at the points of appearance of fatigue cracks in the compartment have been determined for three design versions of the side. It was found that the greatest forces act in the middle of the fore half of the compartment. Calculations of parameters of the long-term distribution of magnitudes of ranges of total equivalent operating stresses according to the Weibull law in the points of occurrence of fatigue cracks for different design versions of the side grillage have been performed. These parameters were determined for the middle of the fore hold of the vessel and for the areas in which maximum values of bending moment ranges are in effect with and without corrosive wear. Values of total fatigue damage and durability of the studied assemblies were determined. Calculations were carried out by nominal stress method, hot spot stress method, and experimental and theoretical method. It was shown that in order to ensure fatigue strength of the assembly under consideration, it is necessary to extend the intermediate frames of the original version of the side structure to the level of the second bottom fixing them to the deck. It is also necessary to attach a cargo platform to the side thus reducing the frame span. As a result, the level of fatigue damage over 25 years of operation will decrease by about 3.5 times. As it was found, approximate consideration of the slamming effect does not significantly increase the amount of fatigue damage to the assembly. The results of the development of recommendations for modernization of the side structure can be implemented both on ships of the 1288 project and on other ships with a transverse side framing system.