SummaryAn 18‐year‐old Saxon Warmblood gelding was referred to an equine clinic in the Czech Republic in May 2019 for mild colic. The horse had 7 h of grazing and 30–45 min of exercise every day. At the clinic, physical examination ruled out gastrointestinal disease, while clinical pathology confirmed rhabdomyolysis (creatine kinase 29,088 IU/L; reference range 110–250 IU/L). Because of the suspicion of atypical myopathy (AM), metabolomic analysis of hypoglycin A (HGA), 31 acylcarnitines (ACs) and free carnitine was performed in four dry serum and one blood spot. After laboratory confirmation of AM in the patient studied (HGA: 0.757–0.415 μmol/L, ACs elevation), an incriminated pasture was visited and searched for the source of the toxin. No sycamore (Acer pseudoplatanus) was found in the vicinity of the pasture. However, several box elder (Acer negundo) trees were found, and toxicological analysis revealed HGA in the samaras (7.66–296.00 mg/kg), leaves (2.12–9.39 mg/kg) and seedlings (339.00 mg/kg). Not only sycamore but also the box elder tree can be a potential source of poisoning in horses in Europe, particularly in lowland areas with a warm climate.