We aimed to assess anxiety of children with primary ciliary dyskinesia (PCD) and their primary caregivers at the beginning of Coronavirus disease-2019 (COVID-19) pandemic and change in levels of anxiety in first year with prolongation of pandemic. This was a two-step study; first step was questionnaire-based, conducted via teleconference. In first step, 29 patients and 105 healthy children and their mothers were participated; 25 children with PCD and their mothers were in second step. Demographic characteristics, clinical informations were recorded. Children’s and mothers’ state and trait anxiety levels were assessed and compared. Anxiety levels of mothers of patients were assessed according to clinical characteristics of children. Mothers’ knowledge of COVID-19 and effect of teleconference on their anxiety was evaluated. State anxiety levels in the first year of pandemic of children with PCD and their mothers were also compared. Compared to control group, state anxiety of children in 13-18 age group and trait anxiety of their mothers were lower (p<0.05). In both groups, trait and state anxiety of 13-18 years old children and mothers positively correlated. Trait anxiety of mothers of patients negatively correlated with patients’ FEV1 and MEF25-75. Patients’ mothers reported feeling less anxiety at the end of teleconference. Anxiety of mothers of patients (especially under 9 years old) had increased as pandemic continued. At the beginning of pandemic, children with PCD were less anxious than healthy children, and their mothers had lower trait anxiety than mothers of healthy children. Being followed for chronic disease and obtaining information about COVID-19 may have reduced anxiety of children with PCD and their mothers. However, as pandemic continues, need to protect their children with PCD from infection, especially of mothers with younger children, may have raised their concerns.