BackgroundThe objectives were to identify 1) the clinician and child characteristics associated with; 2) clinical management decisions following from, and; 3) the prognostic value of; a clinician’s ‘gut feeling something is wrong’ for children presenting to primary care with acute cough and respiratory tract infection (RTI).MethodsMulticentre prospective cohort study where 518 primary care clinicians across 244 general practices in England assessed 8394 children aged ≥3 months and < 16 years for acute cough and RTI. The main outcome measures were: Self-reported clinician ‘gut feeling’; clinician management decisions (antibiotic prescribing, referral for acute admission); and child’s prognosis (reconsultation with evidence of illness deterioration, hospital admission in the 30 days following recruitment).ResultsClinician years since qualification, parent reported symptoms (illness severity score ≥ 7/10, severe fever < 24 h, low energy, shortness of breath) and clinical examination findings (crackles/ crepitations on chest auscultation, recession, pallor, bronchial breathing, wheeze, temperature ≥ 37.8 °C, tachypnoea and inflamed pharynx) independently contributed towards a clinician ‘gut feeling that something was wrong’. ‘Gut feeling’ was independently associated with increased antibiotic prescribing and referral for secondary care assessment. After adjustment for other associated factors, gut feeling was not associated with reconsultations or hospital admissions.ConclusionsClinicians were more likely to report a gut feeling something is wrong, when they were more experienced or when children were more unwell. Gut feeling is independently and strongly associated with antibiotic prescribing and referral to secondary care, but not with two indicators of poor child health.Electronic supplementary materialThe online version of this article (10.1186/s12875-018-0716-7) contains supplementary material, which is available to authorized users.