We performed a study in three Italian regions to evaluate the association between provided recommendations and immunization uptake of the two influenza vaccines in children with chronic diseases. We interviewed families of 119 at-risk children, collecting information regarding recommendations and immunizations against pandemic and seasonal influenza. In total 60.5% of children had received seasonal influenza vaccine, 38.7% had received pandemic influenza vaccine and 33.6% had not been vaccinated. The majority of immunized children had received specific recommendations by a physician. Physicians involved in the management of children with chronic diseases should actively recommend influenza immunization.