The aim of this review is to summarise the main causes of poor welfare in intensively reared dairy cows. Intensive farming systems are considered, both from a structural and a managerial point of view, for their constraints that may limit animal welfare: possible physical activity; acceptable interactions with humans and other animals; feeding and watering, protection from climate, parasites, and diseases. The dairy farms managed according to the organic rules do not always guarantee, per se, better welfare conditions; organic or low input dairy farming needs to consider the right interaction among cattle breed and herd management, focusing on the actual quality of feedstuffs meet face cow requirements. The considered structural aspects evidence how special care must be given to the rest area (straw yard or cubicle); to the floors that should be not too hard or abrasive and not slippery; to the cubicle bedding material to ensure hygiene, softness, and dryness; to the feeding (and watering) area to reduce conflicts; to a microclimate control system, to avoid heat stress during summer time. The importance of proper management for animal welfare is evidenced for buildings and equipment, to have clean and comfortable stables and well functioning milking machines; nutritive and storage quality of feeds; diet suitability (energy, protein, physically efficient fibre, buffers etc.), in the different phases of a dairy cow’s life (dry period, close-up, transition, and lactation); feed distribution (frequency and time), and 24h availability. Special attention has to be paid to the social aspects, regarding both animal competition (stocking density, group size), and human/animal interactions (methods of management and manipulation). The interaction between welfare and health requires special attention. Poor welfare can cause immune depression, thus increasing the risk of disease. In turn, any disease that causes an inflammatory response may determine depression, anorexia, an increase in temperature, and metabolic pathways deviation, with a worsening of the overall sense of well-being.