Ciliated cells in the airway epithelium generate mucus streams to remove extraneous particles and microorganisms by beating the motile cilia. This defense mechanism is crucial for maintaining homeostasis and preventing infection in the airway. Conventional methods to assess ciliary beating have revealed that rapid (>10 times per second) and metachronal beating of cilia enables efficient mucus transport. Cilia are oriented to excrete mucus toward the outside of the body. However, conventional methods to directly observe ciliary movements uses transmitted light, which requires translucent samples. Sliced or fragmented tissues are used to observe ciliary movements in thick human airway tissues. Therefore, conventional methods are unsuitable for assessing in situ orientation of ciliary movements. The orientation of ciliary beating can be indirectly analyzed by tracking particles spread onto the epithelium; however, the particles are not efficiently transported by immature cilia. To address this issue, we developed a method for labeling airway motile cilia with fluorescently labeled wheat germ agglutinin (FL-WGA). The new method enables microscopic observation of ciliary movements without slicing or fragmenting the airway tissues. Since the airway epithelium is observed from the apical side, in situ orientation of ciliary beating can be analyzed using this method. Additionally, epithelial damage, and the number and maturity of cilia can be assessed during the observation of ciliary beating. The new method, in combination with other methods, can provide more comprehensive data regarding ciliary movements.