Major concerns about the quality of basic hospital care for children have been raised in developing countries, but no formal assessment applying international standards has been done in the Commonwealth of Independent States. We assessed 17 hospitals in Kazakhstan, the Republic of Moldova, and the Russian Federation with a generic WHO hospital assessment framework adapted for use in the WHO European region. WHO management guidelines for paediatric care in peripheral hospitals were used as standards. Hospital access for children was generally good. Good health networks existed, and skilled and committed doctors cared for children. Case-fatality rates were low. However, unnecessary and lengthy hospital stays were common, and most children received excessive and ineffective treatment (in one country median number of drugs prescribed concurrently was 5, IQR 2-6). Several conditions were systematically overdiagnosed, especially neurological disease, or overinvestigated, such as acute diarrhoea. Reasons for these practices included absence of clear evidence-based clinical guidelines, regulations tying duration of admission to financial reimbursement, generalisation of disease-control methods from rare problems to common illnesses, and regulations maintaining financial and professional status of some subspecialties. Many disincentives to efficient practice existed. To improve quality of hospital care for children in the Commonwealth of Independent States, several issues must be addressed, including: adoption of international guidelines for inpatient management; complementary guidelines for outpatient management; reforms to health regulations governing admission and discharge criteria; improvement of quality of training, availability of medical information, and systems to promote and certify quality of care.