Objectives Felis catus papillomavirus type 2 (FcaPV-2) commonly infects the skin of domestic cats, and mounting evidence suggests that the virus could be involved in a subset of feline skin cancers. The reason why some cats develop FcaPV-2-induced disease and others do not is currently unknown. However, it has been shown that kittens in different litters have markedly different FcaPV-2 DNA loads and the aim of this study was to determine whether these differences could be due to inherent differences in susceptibility to infection. Such differences could potentially explain why only a small proportion of cats develop FcaPV-2-associated skin disease. Methods Repeated skin swabs were taken to measure FcaPV-2 DNA loads in queens and kittens in a research colony. The kittens either stayed in their original litters or were moved between litters; eventually, all of the kittens were housed together. A subset of samples was also analysed for FcaPV-2 mRNA. Results While there were initially large differences in FcaPV-2 DNA loads between litters of kittens, these differences disappeared when the kittens were moved between litters or housed together. Importantly, the viral DNA loads changed too rapidly to be due to the acquisition or clearance of infection. In contrast, the differences in viral DNA loads between the different queens were sustained throughout the experiment. FcaPV-2 mRNA was also detected in samples from 1- to 8-day-old kittens. Conclusions and relevance The results suggest that the FcaPV-2 DNA load in a swab sample from an individual kitten largely reflects the overall level of FcaPV-2 shedding in the group of in-contact cats, rather than the infection status of the individual kitten. Therefore, there was no evidence for inherent differences in susceptibility to infection. However, the finding of FcaPV-2 mRNA suggests that at least some kittens do become infected with FcaPV-2 early in life.