The study of the mechanisms of aging, a complex biological process, remains a pressing issue. Aging involves not only functional and structural alterations in organs but also the mobilization of adaptive mechanisms. The aim of this study was to identify both general and tissue-specific features of ultrastructural changes in different organs of old (20 months) rats. Liver, heart, and lung tissue sections from rats of various ages were examined by electron microscopy. Morphometric calculations were performed using the Image Tool Version 3 software (USA) on 130–150 microscopic fields for each effect studied. In the liver tissue of old rats, an increased number of areas containing granular endoplasmic reticulum with preserved bound ribosomes and mitochondria-associated membranes was observed; numerous glycogen granules were also found. In the myocardium, the formation of micromitochondria was noted, which may reflect compensatory responses aimed at maintaining the energy capacity of the mitochondrial apparatus. In the lung tissue, a significant number of dilated endoplasmic reticulum cisterns were found, along with signs of mitophagy activation. Such activation is ensured by the formation of numerous primary lysosomes with subsequent formation of a secondary autophagic type. Thus, age-related ultrastructural changes are organ-specific and include both pathological alterations and compensatory responses.