Hyperammonemia, a life-threatening condition, is a common complication of a wide variety of disorders as well as a primary etiologic agent of hepatic encephalopathy (HE), a decline in brain functions secondary to advanced liver dysfunction and failure. Measurements of ammonia in blood were first described more than a century ago and since then, several new methods have been proposed for the determination of ammonia in biological fluids. The direct enzymatic determination of ammonia in plasma is nowadays the most commonly used ammonia assay in clinical chemistry. Here, we summarize the current recommendations for the quantification of ammonia in biological fluids, in particular in plasma, by listing sample pre-analysis handling requisites and principal potential contaminants. Ammonia homeostasis is a whole-body dynamic process tightly regulated. Assessing the altered accumulation of ammonia and disrupted metabolism in the different organ/systems tissues is important for increasing our knowledge of the underlying disturbed molecular mechanisms in a series of pathologies. Therefore, the establishment of adequate methodologies for the detection of ammonia in mammalian tissue is of paramount importance. Herein, we provide a detailed description of a method for detecting ammonia in formalin-fixed paraffin-embedded mammalian tissue. This histological-based method takes advantage of the Nessler colorimetric reaction to detect ammonia analyzing this metabolite distribution in specific regions of interest of the mammalian brain, liver, and other organs of interest.