Parents of children with a Congenital Anomaly or Cerebral Palsy identified needs when interacting with health services. Children with a Congenital Anomaly (CA) or Cerebral Palsy (CP) have special health needs, with frequent use of healthcare services (HCS). Evidence suggests that parents positive engagement with healthcare providers is associated with health outcomes improvement and reduced healthcare costs. A mixed-method modify research design was employed in a cross-sectional study with a convenience sample of parents of children diagnosed with CA (severe heart anomalies; spina bifida; orofacial clefts or Down syndrome) and/or CP. A semi-structured online questionnaire was sent by web link to focal points of five institutions in Portugal. Data was analysed through thematic content analysis (open-ended questions) and descriptive analysis (closed-ended questions). A total of 254 questionnaires were returned. Findings support the need for better collaboration between services and professionals and the importance of information - which elicited apparently divergent results. Of the 15 closed items, two were less frequently rated as a reality within HCS: receiving written information (51.2’) and being encouraged to ask questions (42.7%). Inversely, most parents believed that the health services and professionals taught them how to care for one’s child (81.6%) and felt to be informed them about what affects the child’s development (74.4%). Thematic analysis indicated that parents perceived lack of information and professional’s lack of knowledge and training about their child specific conditions. The mixed methods results indicated perceived lack of collaboration between health services and professionals. On the other hand, while parent perceive that HCS provided enough information on child health care and illness, they felt professional specific knowledge on the child condition as insufficient. This apparent divergent result may be related to parents perceiving health care to emphasize acute illness in detriment of the long-term management of chronic conditions and disabilities.