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Highlights • High prevalence of intestinal parasite colonisation; all were asymptomatic. • High prevalence of MRSA; low prevalence of ESBL and CPO. • Recommend attention to antimicrobial resistance when attending to Syrian refugees. • Recommend no routine screening for parasites in asymptomatic adult Syrian refugees., Introduction Concerns have been raised regarding the emergence of antimicrobial-resistance and parasitic infections in the European refugee population. Here, we estimated the prevalence of intestinal parasites and selected antimicrobial-resistant bacteria in newly arrived asylum seekers in Denmark. Materials and methods Using a cross-sectional one-stage cluster sample design, adult Syrian asylum seekers were included upon arrival in Denmark. Faecal samples were collected and tested for ova and parasites, extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E) and carbapenemase-producing organisms (CPO). Throat swabs were collected and analysed for methicillin-resistant Staphylococcus aureus (MRSA) and Corynebacterium diphtheriae. Results We invited 121 eligible individuals (20% of the source population) from six different asylum centres to participate, of whom 113 agreed. Throat swabs and faecal samples were received from 104 and 48 participants, respectively. Seven individuals did not provide enough material for the entire panel of faecal analyses. Three individuals (7.3%, 95%CI: 2.5–19.4%) were colonised with Giardia intestinalis and 28 (68.3%, 95%CI: 53.0–80.4%) with Blastocystis sp. (subtypes 1 [n = 5], 2 [n = 9] and 3 [n = 14]). Seven individuals (6.7%, 95%CI: 3.3–13.3%) were colonised with MRSA and one with ESBL-E. None had CPO or Corynebacterium diphtheriae and none reported any gastro-intestinal symptoms. Discussion Even with the most conservative estimates, the prevalence of Giardia intestinalis, Blastocystis sp. and MRSA was high in this asymptomatic refugee population. Conclusions We highlight the importance of raised awareness of antimicrobial-resistant bacteria when attending to newly arrived Syrian refugees. Meanwhile, our data suggest that routine screening for intestinal parasites in this population is of limited clinical relevance.