Despite the growing availability of noninvasive and faster diagnostic modalities, biopsy remains an important tool in the diagnosis and management of liver diseases. However, it is not uncommon that liver biopsies reveal normal or near normal histologic findings in patients with abnormal liver biochemistries, elevated autoantibodies, clinical findings suggestive of portal hypertension, systemic autoimmune or inflammatory diseases, hepatomegaly, cirrhosis by imaging, or other indications. These scenarios present significant diagnostic challenges and are rarely discussed in detail in the literature or textbooks. This article aims to provide a comprehensive review of a group of selected rare liver diseases, with a focus on metabolic, storage and inclusion disorders, that may exhibit a near-normal histology on biopsy. By recognizing subtle histologic features and correlating with clinical history, laboratory results and imaging findings, it is often possible to narrow down the differential diagnosis. In many cases, this integrative approach can yield a definitive diagnosis, allowing for tailored treatment and better patient outcomes.