Synaesthesia is a neurodevelopmental trait that causes unusual sensory experiences (e.g., perceiving colours when reading letters and numbers). Our paper represents the first evidence that synaesthesia can impact negatively on children’s well-being, and that there are likely to be important mental health co-morbidities for children with synaesthesia. We recruited 76 synaesthetes aged 6-10 years who had one of two types of synaesthesia (grapheme-colour synaesthesia and sequence-personality synaesthesia), and compared them to almost one thousand matched non-synaesthete controls. We tested children’s wellbeing with two different measures, and found a significant relationship between synaesthesia and affect (i.e., mood), and also between synaesthesia and anxiety. Children with synaesthesia showed evidence suggesting significantly higher rates of Anxiety Disorder, and also displayed a type of mood-moderation in demonstrating fewer extremes of emotion (i.e., significantly fewer negative feelings such as fear, but also significantly fewer positive feelings such as joy). We discuss our results with reference to the emotional moderation of alexithymia (the inability to recognize or describe one's own emotions), and to a set of known links between alexithymia, anxiety, autism and synaesthesia.