The role of pets (dogs and cats in particular) in human society has changed in recent years. Nowadays pets are an integral part of the human family and this aspect has many social and emotional implications. For their positive effects on human health, pets are also employed in some special and therapeutic activities known by the generic term of “Pet Therapy”. In these programmes the animal becomes an integral part of the therapeutic plan in order to induce some physical, social, emotional, and cognitive improvements in human patients. However, the close bond between companion animals and man is not always the herald of beneficial effects. Sometimes the welfare of pets may be compromised by distress due to many factors, mostly related to the environment and to management by humans. Both behavioural and physiological variables may be analysed in order to evaluate welfare level in pets. Reduced welfare may be indicated by the onset of some behavioural problems, which have usually a multifactorial aetiology, related both to the genetic individual basis and environmental factors. Physiological variables which may be analysed in order to evaluate pet welfare include hormone levels, mainly related to the HPA (hypothalamus-pituitary-adrenal- axis) and to the immune systems activations. Behavioural problems may also lead to the relinquishment of pets to shelters. Animals housed in rescue shelters cannot display their ethogram and show behavioural and physiological signs of distress. Thus it is very important to improve the human-pet relationship both by educating owners and reducing the number of stray animals, in accordance with the indications of the European Convention for the Protection of Pet Animals stated at Strasbourg in 1987, mainly as regards pet breeding and welfare. Humans have to realise that adopting pets implies the responsibility to care for their health and welfare, avoiding undue stress in the living environment and improving the human-pet relationship.