The usefulness of various segment and cell-type specific antibody, lectin and functional markers in the study of cystic renal lesions was evaluated. For this purpose, kidneys from recessive polycystic kidney disease (RPKD), thought to involve mainly the collecting ducts, and cystic kidneys of Meckel's syndrome (MS), which show dilation randomly along the nephron, were studied. The segment (and differentiation-stage)-specific anti-brush-border (specific for proximal tubules) antibodies stained morphologically normal proximal tubules, failed to react with cyst wall epithelium in RPKD, but readily stained some cysts in MS. Immunostaining for Tamm-Horsfall glycoprotein (distal tubules) similarly revealed normal tubular profiles, and also stained moderately dilated tubules, but not the large cysts in either disease type. Lectin markers of the distal tubules and collecting ducts (peanut agglutinin, Helix pomatia agglutinin and Dolichos biflorus agglutinin) reacted with both dilated tubules and with the cyst walls in RPKD and Meckel kidneys, suggesting that in RPKD, the dilations also occur in the distal nephron in addition to the collecting duct, and in MS in any part of the renal tubule. The cell type-specific functional marker of the collecting duct, anti-NaK-ATPase reactivity (found in principal cells) could be seen in RPKD but not in Meckel kidney cysts, suggesting a minor involvement of principal cells in MS. Consistent with this, only occasional carbonic anhydrase (found in intercalated cells) or band 3 (bicarbonate-chloride exchanger molecule of intercalated cells) of collecting ducts positive cells in the cysts could be seen, suggesting that intercalated cells are only sparsely seen in these lesions. The results show the usefulness of a panel of independent markers in studying the segment, cell-type and function-specific features of renal cystic lesions as a basis for their classification.