Equine endometrial degeneration is diagnosed by microscopy of an endometrial biopsy but it is uncertain if findings in a single biopsy represent the state of the entire endometrium. Previous studies have compared samples from multiple sites but conclusions are inconsistent. Further clarification is therefore needed. In this study, presence and characteristics of endometrial degeneration were compared in two full thickness specimens from the ventral base of both uterine horns, obtained post mortem from cyclic mares (n = 82). Hematoxylin and eosin-stained sections were blinded evaluated for periglandular fibrosis, glandular nests, dilated glands, glandular dilation, excessive lymphatic vessels, and lymphatic lacunae. Each section was also assigned to a modified Kenney and Doig categorization. Statistical analysis included multiple logistic regression models for fraction of mares with disagreement in the modified Kenney and Doig category and fraction of mares with disagreement for each parameter, multiple generalized linear regression models for fraction of parameters with disagreement, and equivalence tests for agreement of a cumulative score of degenerative parameters. Possible effect of age, mare type and estrous cycle stage were included in the analyses. For the Kenney and Doig categorization, 49% of the mares had good agreement, 46% had moderate agreement and 5% had poor agreement between the two biopsies. Disagreement in the Kenney and Doig categorization between the two biopsies increased with age (OR = 1.1, P = 0.009). Disagreement within each parameter ranged from 10% of mares (glandular nests), to 31% (periglandular fibroblasts) and 37% (lymphatic lacunae). Disagreement for changes in endometrial glands increased with age (OR = 1.15–1.16, P < 0.040). Several mares (33%) had disagreement in at least two parameters, and the number of parameters with disagreement increased with age (HR = 1.04, P = 0.010). When tested for equivalence, the cumulative scores for paired endometrial samples did not differ for mares younger than 18 years (P = 0.011). In conclusion, the degenerative changes were not uniformly distributed, revealed by a disagreement between paired endometrial samples for individual parameters and for the Kenney and Doig categorization, which increased with age. This suggests that conclusions based on a single biopsy, particularly in mares over 17 years of age, should be interpreted with caution, and evaluation of two biopsies should be considered.