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Abstract Background Acute ocular motility disorders (OMDs) in children admitted to Emergency Department (ED) represents a not so rare condition with a wide spectrum of different etiologies. The emergency physician must be skilled in rapidly identifying patients with potentially life threatening (LT) forms, requiring further diagnostic procedures. The aim of the study was to assess characteristics of children with acute Ocular Motility Disorders (OMDs), and to identify “red flags” for recognition of underlying life-threatening (LT) conditions. Methods A retrospective cohort study evaluated children (2 months-17 years) admitted to a tertiary Emergency Department in 2009–2014. A subgroup analysis was performed comparing children with and without LT conditions. Results Of 192 visits for OMDs, the isolated strabismus occurred most frequently (55.6%), followed by pupil disorders (31.8%), ptosis (5.2%) and combined OMDs (11.5%). The majority of acute OMDs involved no underlying LT conditions (n = 136) and most of them were infants or toddlers (50%). In a multivariable analysis, LT conditions included especially children over 6 years of age, increasing the odds ratio by 2% for each months of age (p = 0.009). LT etiologies were 16 times more likely in combined OMDs (p = 0.018), were over 13 times more likely to report associated extra-ocular signs/symptoms (p = 0.017) and over 50 times more likely to report co-morbidity (p = 0.017). Conclusion OMDs are not an uncommon presentation at ED. Although most of them involve non-LT conditions, the ED physician should consider potential “red flags” for appropriate management of children such as age > 6 years, combined OMDs, extra-ocular symptoms and co-morbidity.