To compare regional conjunctival expression of membrane-associated mucins (MAMs) MUC1, MUC4, and MUC16 in normal and dry eye (DE) subjects. Adults with and without signs and symptoms of DE were recruited. Impression cytology was performed to collect MAMs from four bulbar and upper eyelid palpebral conjunctival regions of both eyes. After protein extraction, samples from both eyes of a single subject were pooled by region, and expression was analyzed using a capillary electrophoresis nano-immunoassay system. The chemiluminescence intensity of each antigen binding signal was calculated after normalization to the total protein amount. Statistical analyses were conducted using GraphPad Prime 9. Samples from thirteen to sixteen DE and seven to eleven normal subjects were analyzed. In normal samples, MUC1 expression from the nasal bulbar conjunctiva was significantly greater than superior (P = 0.004) and inferior (P = 0.005). In DE samples, MUC1 expression was highest superiorly. Significant differences in MUC4 and MUC16 expression were not seen in normal samples. MUC4 and MUC16 expression was upregulated superiorly (P < 0.0001) and inferiorly (P < 0.0001) in DE compared with those regions in normal samples. Although MAMs form a hydrophilic barrier called the glycocalyx, each mucin may have unique functions that are currently unexplored. All MAMs were expressed in the upper palpebral conjunctiva. Increased MUC1 expression nasally in healthy subjects suggests a functional need for increased protection. When comparing DE with normal eyes, upregulation of MUC1 superiorly, and in both MUC4 and MUC16 both superiorly and inferiorly, may indicate a need to decrease eyelid friction during blinking, especially in DE.