BACKGROUND: The fragmentation of healthcare provision has given rise to a wide range of interventions within organizations to improve coordination across levels of care, primarily in high income countries but also in some middle and low-income countries. The aim is to analyze the use of coordination mechanisms in healthcare networks and its implications for the delivery of health care. This is studied from the perspective of health personnel in two countries with different health systems, Colombia and Brazil. METHODS: A qualitative, exploratory and descriptive-interpretative study was conducted, based on a case study of healthcare networks in two municipalities in each country. Individual semi-structured interviews were conducted with a three stage theoretical sample of a) health (112) and administrative (66) professionals of different care levels, and b) managers of providers (42) and insurers (14). A thematic content analysis was conducted, segmented by cases, informant groups and themes. RESULTS: The results show that care coordination mechanisms are poorly implemented in general. However, the results are marginally better in certain segments of the Colombian networks analyzed (ambulatory centres with primary and secondary care co-location owned by or tied to the contributory scheme insurers, and public providers of the subsidized scheme); and in the network of the state capital in Brazil. Professionals point to numerous problems in the use of existing mechanisms, such as the insufficient recording of information in referral forms, low frequency and level of participation in shared clinical sessions, low adherence to the few available clinical guidelines and the lack of or inadequate referral of patients by the patient referral centres, particularly in the Brazilian networks. The absence or limited use of care coordination mechanisms leads, according to informants, to the inadequate follow-up of patients, interruptions in care and duplication of tests. Professionals use informal strategies to try to overcome these limitations. CONCLUSIONS: The results indicate not only the limited implementation of mechanisms for coordination across care levels, but also a limited use of existing mechanisms in the healthcare networks analyzed. This has a negative impact on coordination, efficiency and quality of care. Organizational changes are required in the networks and healthcare systems to address these problems.