Feeding problems are associated with the consumption of a limited amount or restricted variety of foods and often occur in children with gastrointestinal diseases. The majority of studies to date do not use valid and reliable measurements to detect feeding problems. The aim of this cross-sectional study was to assess behavioral and skill-based feeding problems in young children with gastrointestinal diseases by using a well-established parent-reported feeding measure and identify demographic, anthropometric, and environmental factors associated with maladaptive feeding behaviors in this pediatric population. Parents completed the Greek version of the Behavioral Pediatrics Feeding Assessment Scale (BPFAS) and self-reported questionnaires assessing mealtime environment and parental feeding practices. It was found that 18.6% of the sample had abnormal Total Frequency Score (TFS) (frequency of problematic feeding behaviors) and 39.5% had abnormal Total Problem Score (TPS) (number of behaviors perceived as problematic by parents). Younger children, with lower body mass index, lower birth weight, and only children were more likely to have feeding problems. The study showed that parent-reported feeding problems are increased in young children with gastrointestinal diseases and are associated with specific aspects of mealtime environment and parental feeding practices.