The confined environment of the dog shelter, particularly over extensive time-periods can impact severely on welfare. Surveillance and assessment are therefore essential components of the welfare protocol. The aim of this study was to generate a descriptive analysis of a sample of Italian long-term shelters and identify potential hazards regarding the welfare of shelter dogs. This was achieved through application of the Shelter Quality Protocol (SQP) to link income/outcome variables and the inclusion of sixty-four long-term shelters in Italy. Descriptive and logistic regression analyses were conducted. Key findings showed feeding regime, type of diet and access to outdoor area to be significantly associated with inadequate body condition score (BCS). The probability of observing skin lesions was shown to be influenced by bedding inadequacy and bedding type. Limiting beds to one per dog and utilising clean bedding materials was significantly associated with a reduced probability of observing dirty/wet dogs. Protection from adverse weather conditions and inadequate bedding were significantly associated with the manifestation of polypnea. Non-existent dog training facilities, outdoor access or leash walking were all found to significantly increase the likelihood of fearful or aggressive attitudes to people. Outdoor access also, in conjunction with feeding regime, was associated with the presence of diarrhoea. The SQP proved useful in identifying welfare hazards, both as regards shelter environment and shelter management. Identification of these hazards creates the opportunity for interventions to be applied, minimising the risks and improving the welfare of long-term shelter dogs.