Canine coronavirus (CCoV) is an enveloped RNA virus, responsible for gastrointestinal infection in dogs. To date, two different CCoV genotypes have been recognized, CCoV type I and CCoV type II. Recently, CCoV type II strains of potential recombinant origin with transmissible gastroenteritis virus (TGEV) were detected and characterized as a new subtype (CCoV-IIb) of canine coronavirus, in order to be differentiated from the "classical" CCoV type II strains (CCoV-IIa). In the present study, two CCoV-IIb strains were detected in the faeces and internal organs of two puppies, which died after presenting gastrointestinal symptoms. Mixed infection of both subtypes (CCoV-IIa/IIb) was detected in the faeces, while only CCoV-IIb was detected in the organs. Puppies were also infected by canine parvovirus type 2 (CPV-2). Both CCoV-IIb strains were isolated on cell cultures and subjected to sequence analysis and phylogeny. By means of RT-PCR and real time RT-PCR assays, tissue distribution and quantitation of viral loads took place. These cases represent the first description of tissue distribution and quantitation of CCoV-IIb strains, detected in the organs. The detection of CCoV-IIa strains, which is restricted to the faeces, suggests that CCoV-IIb strains may have an advantage in disseminating throughout a dog with CPV-2 coinfection, in contrast to common enteric CCoV-IIa strains.