We report herein the results of the cross-cultural adaptation and validation into the Croatian language of the parent's version of two health related quality of life instruments. The Childhood Health Assessment Questionnaire (CHAQ) is a disease specific health instrument that measures functional ability in daily living activities in children with juvenile idiopathic arthritis (JIA). The Child Health Questionnaire (CHQ) is a generic health instrument designed to capture the physical and psychosocial well-being of children independently from the underlying disease. The Croatian CHAQ-CHQ were fully validated with 3 forward and 3 backward translations. A total of 139 subjects were enrolled: 75 patients with JIA (19% systemic onset, 20% polyarticular onset, 17% extended oligoarticular subtype, and 44% persistent oligoarticular subtype) and 64 healthy children. CHAQ clinically discriminated between healthy subjects and JIA patients, with the polyarticular and extended oligoarticular subtypes having a higher degree of disability, pain, and a lower overall well-being when compared to their healthy peers. Also the CHQ clinically discriminated between healthy subjects and JIA patients, with the polyarticular onset and extended oligoarticular subtypes having a lower physical and psychosocial well-being when compared to their healthy peers. In conclusion the Croatian version of the CHAQ-CHQ is a reliable, and valid tool for the functional, physical and psychosocial assessment of children with JIA.