Non-right handedness has been associated with allergic diseases and asthma. Infantile diabetes, too, has been associated with non-right handedness but, to date, data are more consistent on a link between left handedness and asthma than on diabetes. We surmised that mixed handedness, as an indicator of neurodevelopmental disturbance of brain laterality, rather than left handedness is more prevalent among children with asthma and diabetes mellitus. A total of 100 families with a child or an adolescent diagnosed with infantile asthma (n = 50) or diabetes mellitus type 1 (n = 50) attending the Paediatric Clinic of the ‘Brotzu’ Hospital in Cagliari (Italy) in 2006 agreed to participate in the study. The Annett Hand Preference Questionnaire was used to test handedness. Compared with 99 same-age and -sex controls, cases were marginally less likely to be right handed (71% vs. 86%; OR = 0.82, 95% CI = 0.54–1.25), and statistically more likely to be mixed handed (20% vs. 6%; OR = 3.30, 95% CI = 1.27–8.56) than controls: χ2 = 8.84, d.f. = 2, p = 0.01. Children with asthma or diabetes did not differ from controls by season of birth; however, mixed-handed (n = 12, 46%) and left-handed (n = 6, 35%) children were statistically more likely to be born in winter as against the other seasons than those who were right handed (n = 36, 23%). Severity was also marginally related to the chance of being classified as non-right handed. People with a genetic predisposition to immune disorders could be more likely to have been negatively affected by infection and inflammation during fetal life, thus developing a deviation in handedness during neurodevelopment, as well as suffering the consequence of disordered immunity during childhood, such as allergic reactions (asthma) and immune-mediated damage to specific internal organs (diabetes type 1).