Abstract. We adapted the critical angle method for measuring rough surfaces under partial contact to acquire an in vivo skin refractive index (RI). Assuming that the total reflection is the simple sum of reflection from areas that are in contact and reflection from those that are not in contact, the RI can be estimated even for partial contact with a rough surface. We found that cheek skin is sufficiently soft that a sufficiently large area can be in contact and that the critical angle was detectable. The RIs of the cheeks of adult females were measured. The RI range was about 1.51 to 1.53, at a wavelength of 550 nm, without considering systematic errors. The RIs of cheeks are significantly correlated with their conductance, which corresponds to their water content. We determined the relationship between the RI and conductance within the variation of skin under normal conditions; this relationship was theoretically obtained in previous studies. In the present study, a direct in vivo measurement method was developed that enabled us to measure the RI in daily life, although this method contains errors for several reasons, including disregarding absorption. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI.