There is a recognized need to raise evidence on how to adopt human rights-based approaches (HRBAs) to health and to assess their impact. In 2013 and 2014, the World Health Organization (WHO) Regional Office for Europe used a set of tools to assess and improve the situation of children’s rights in 11 hospitals in Kyrgyzstan, 10 hospitals in Tajikistan, and 21 hospitals in Moldova, by applying a HRBA to health, taking as a reference the Convention on the Rights of the Child (CRC). The assessment results show a similar situation across countries in some areas, and more or less significant variation in others. Common gaps include the need to improve adolescent-friendly health services, the rights to privacy and play; and infrastructure and equipment. In Kyrgyzstan and Tajikistan, a second round of assessment, was carried out, which showed an effective change in several areas, whilst other areas showed persistent gaps. Moldova did not carry out a second round of assessment. Involving children and parents in the assessment was crucial to obtain more reliable data; the project showed how to use the CRC as a framework to improve quality of care for children (QoC); and the tools were proven useful for self-assessment.