The aim of this study was to investigate pathomorphological changes in the duodenum, jejunum, ileum, and caecum of Japanese quails naturally infected with Eimeria tsunodai. Samples of the intestines were collected from 6-week-old cockerels and hens before laying and from laying quails aged 12, 24, and 48 weeks. The tissue sections were stained with haematoxylin and eosin, PAS method according to McManus, and Ziehl-Neelsen method. Morphometric and morphological analyses of coccidia revealed that Eimeria tsunodai was responsible for the infection. Different developmental stages of the coccidia were observed almost exclusively in the caecum, and they led to the complete damage of caecal mucosa. The main changes observed in the caecum involved mucosal damage, atrophy of the folds and crypts, and mucosal desquamation. No significant inflammation changes were detected. The degree of damage to caecal mucosa increased with age and the greatest damage was noted at the age of 48 weeks. Eimeria tsunodai infections occur in Japanese quails during the entire laying period. Different developmental stages of coccidia are responsible for total damage to caecal mucosa.