Background: Equine neonatology focuses mainly on perinatal period from the terminal phase of pregnancy throughout the first few weeks of life. The delayed recognition of abnormalities in the early postpartum period can lead to severe consequences, or it may affect the future performance of the expected equine athlete. This specialty has gained attention in the last 30-40 years close proximity to the substantial Thoroughbred-breeding centres of the world. Objectives: The aim of this review is to provide a practical approach to equine veterinarians, students, horse breeders and owners about the hallmarks of the most important disease entities in this age-group of foals using our own experiences and published data. Results and Discussion: In our second article we summarize and discuss disorders of the gastrointestinal tract, the urinary, locomotive, nervous, endocrine and immune systems of the young foals, based on the latest literature. The following diseases are detailed: meconeum impaction, gastric ulcers, different diarrhoeal diseases of foals, uropoeritoneum, septic synovitis and osteomyelitis, white muscle disease, perinatal asphyxia syndrome, meningitis and meningoencephalitis, congenital defects of the nervous system (such as cerebellar abiotrophy, levander foal syndrome, occipito-atlantoaxial malformation, juvenile idiopathic epilepsy), hypothalamic-pituitary-adrenal axis dysfunction, goiter, hypothyreosis, neonatal isoerythrolysis, severe combined immunodeficiency, immune-mediated thrombocytopenia. The authors will discuss the neonatal septicaemia in a later manuscript.