Neonatal hypotonia is a condition which appears to expand continually. Since the 1980s new clinical disorders, such as mitochondriopathies, peroxisomal diseases, disorders of the beta-oxidation of fatty acids, congenital myasthenic syndromes and botulism in infants have been described. At the same time, considerable progress has been made in the understanding of congenital myopathies, congenital muscular dystrophy and neonatal myotonic dystrophy. In this review we describe the most relevant conditions in which hypotonia is seen, and give guidelines for orientation in the study of newborn babies with this condition. We emphasize the importance of a clinical approach based on the family history (myotonic dystrophy, transitory neonatal myasthenia), the prenatal history (fetal movements, polyhydramnios) and neurological examination (facial diplegia, lingual fasciculations, arthrogryposis, respiratory difficulty) which permits early completion of studies, including muscle biopsy--very useful in the neonatal period--and genetic analysis. This allows the prognosis of the condition to be established early so that timely and effective genetic counselling may be given to the parents, avoiding recurrence of the serious morbi-mortality of many of these conditions.