A cross-sectional survey study was designed to gather information on the use of dietary supplements by Spanish pediatricians. The study questionnaire was completed by 433 pediatricians (62% men, mean age 52.5 years) throughout the country. They also provided data on 10 of their patients (n = 4304) in which synbiotics, immune stimulants, and omega-3 polyunsaturated fatty acids (PUFAs) had been prescribed. Synbiotics were used by 92% of pediatricians, immune stimulants by 80.4%, and omega-3 PUFAs by 75.1%. Synbiotics were mainly used combined with antibiotics (92.6%) and for gastrointestinal disorders (91.2%), immune stimulants to enhance defenses and cold prevention (87.1%), and omega-3 PUFAs to improve symptoms of attention-deficit hyperactivity disorder (ADHD) (84.8%) and concentration (80.1%). Confidence and previous experience with the product (51.6%), composition and indications of the product (43.1%), and tolerability (39.9%) were main factors involved in decision-making. Children treated with omega-3 supplements were significantly older (mean age 7.6 (3.0) years) than those treated with synbiotics (3.9 (3.9) years) or immune stimulants (3.4 (2.8) years) (P < 0.001). Short duration of treatment (<1 month) was significantly more common in the synbiotics group (90.5%), whereas longer duration of treatment (>3 months) was more frequent in the omega-3 group (79.1%). In the immune stimulants group, 60.4% of patients were treated for a period between 1 and 3 months. Clinical improvement was rated by participants as "a lot" in 39% of cases and as "quite" improvement in 50.6%. The overall level of satisfaction was rated as "very satisfied" by 52.1% of participants and as "quite satisfied" by 40.9%. The results show that the use of dietary supplements to improve different conditions, particularly minor disorders, is a widespread clinical practice among Spanish pediatricians. Administration regimens for the three types of supplements, synbiotics, immune stimulants, and omega-3 PUFAs, were consistent with guideline recommendations.