In vitro airway specimens are widely used to evaluate airway ciliary function. However, the function of in vitro ciliated cells may be far different from their actual in vivo physiological conditions. Due to the lack of a valid technique, direct images of in vivo airway ciliary motion have never been captured and analyzed before. This study aims to examine nasal ciliary motion in living guinea pigs with comparison to in vitro observation. Nasal septum mucosa was exposed in anaesthetized guinea pigs and directly examined using a digital microscopy system. The study included three parts: (1) measurement of ciliary beat frequency (CBF) of nasal mucosa at room temperature in living guinea pigs and immediately after death, and in dissected mucosa specimens/cells for comparison; (2) monitoring of nasal ciliary motion, CBF, and ciliary beat distance (CBD) over 12 h in both living guinea pigs and dissected mucosa specimens/cells; and (3) measurement of ciliary motion changes in responses to temperature variations. Compared with when the animal was alive, the CBF after death and in dissected mucosa specimens/cells was lower by about 20% ( P < 0.05). CBF and CBD variation in living guinea pigs was within 10% over time. The slope of CBF/temperature profile was 0.18 ± 0.01 Hz/°C in living guinea pigs, 0.51 ± 0.02 Hz/°C for dissected mucosa specimens, and 0.48 ± 0.03 Hz/°C for isolated ciliary cells. The technique described in this study makes it feasible to study ciliary motion in living animals using the digital microscope system. Ciliary function changes immediately after death. Ciliary motion in a living animal is more stable over time and has a different response to temperature change as compared with in vitro observation results. Impact statement Cilia play an important role in the airway defense mechanism. So far, studies on ciliary function have mainly been based on in vitro methods. Images of in vivo ciliary motion are very difficult to capture. In this study, we describe a novel approach to observe and analyze nasal ciliary motion in living animals with comparison to in vitro observation. Such images of ciliary motion from living animals have not been reported to date. The result of the study indicates that in vivo ciliary physiological function differs from ex vivo and in vitro conditions in many ways, such as the stability over time and response to temperature variation. This is a good foundation for further in vivo analysis of airway ciliary physiological function in animals as well as humans.