Here we present a detailed morphological description of the alligator (Alligator mississippiensis) kidney and nephron. We present a series of histological, histochemical, and immunohistochemical markers that clearly define the seven regions of the alligator nephron. The alligator kidney is composed of many paired (mirrored) lobules on each kidney (lobe). Single nephrons span the width of lobules three times. The fine structure of glomeruli, lying in rows spanning the height of the lobule, is resolved by periodic acid methionine silver (PAMS) and periodic acid Schiff 's (PAS) histochemistry. Glomeruli are connected to the proximal tubule (PT) via a neck segment. The PT is alcian blue-negative, making it distinct from the distal tubule (DT), connecting segment (CS), and collecting duct (CD). The PT is clearly identifiable by a PAS-positive brush border membrane. The PT is connected to the DT via an intermediate segment (IS) that makes a 180 turn to connect these tubules. PAMS-positive material is found in the lumens of the PT, IS, and DT. Also, PAMS-positive granules are found in the DT, CS, and CD. Immunolocalization of the Na þ , K þ -ATPase to the basolateral membrane of the DT, CS, and CD suggests a role of this enzyme in driving primary and secondary transport processes in these segments, including bicarbonate transport into the lumen of the DT (leading to an alkaline urine). Through the techniques described here, we have identified a series of distinct markers to be used by pathologists, veterinarians, and researchers to easily identify alligator nephron segments. Anat Rec, 292:1670Rec, 292: -1676Rec, 292: , 2009. V V C 2009 Wiley-Liss, Inc.Key words: Alligator mississippiensis; kidney; nephron; histochemistry; Na þ , K þ -ATPaseThe kidneys' primary functions, the excretion of nitrogenous wastes and the maintenance of water and ion balance, are achieved through three fundamental mechanisms: glomerular filtration, tubular reabsorption, and secretion. To understand these physiological processes, a description of the morphological structures and kidney cell types is integral. Kidneys from various vertebrate species have been well investigated (Dantzler, 1980;Dantzler and Braun, 1980;Schmidt-Nielsen, 1988;Braun, 1998); whereas, knowledge of the crocodilian kidney is more limited. Previous studies of alligator nephrons have investigated general morphology (Huber, 1917), general nephron composition (Ventura et al.,