The availability of novel technologies, such as tandem-mass-spectrometry (MS/MS) and DNA analysis, has expanded tremendously the number of genetic conditions that can be diagnosed through neonatal screening programs at birth, including conditions that cannot be treated nor prevented, or that will become manifest only later in life, or that identify individuals that are only at an increased risk of multifactorial conditions. This has increased the number and complexity of ethical problems related to newborn screening programs, creating considerable confusion and generating controversies and ethical concerns. The experience so far gained indicates that, besides the incomplete knowledge of many aspects of the conditions to be identified, the majority of screening programs do not pay sufficient attention to the problems of communication, information and counselling of the parents. Therefore, communication must be substantially improved if we wish to increase the efficiency of such programs and avoid possible unwanted side effects. Furthermore, ethical issues should receive more attention and consideration for a better and more complete understanding of the overall impact of neonatal screening programs. This more extensive and ethically correct approach should allow us to find an optimal equilibrium between the potential benefits and the possible damages deriving from neonatal screening programs.