Background: Turkey hosts nearly four million refugees and more than 95 percent live in urban areas. Living in urban settings pose different challenges and opportunities than living in camps. This study aimed to assess mental health problems and barriers to accessing mental health care among Syrian refugees in urban areas of Turkey. The study used a mixed-methods approach. Quantitative data were collected by a face-to-face survey among 420 Syrian refugees in Ankara, whereas qualitative data were collected via in-depth interviews with 10 health care providers and 10 health policy makers.Discussion: In our case, the main challenges in conducting research with refugees were collecting data from a highly traumatized population, difficulties with contacting undocumented asylum seekers including trust issues and the fear of deportation, the risk of secondary traumatization among data collectors, and the bureaucracy during study approval processes. Targeting a representative sample was not feasible, because of the lack of publicly available demographic data on a district level, presence of undocumented asylum seekers and high mobility among the registered refugees. Although respondents with significant psychological symptoms were routinely referred to available mental health services, we were not able to do the same for unregistered refugees with problems in accessing health care. Language/alphabet differences and differing dialects of Arabic posed another challenge in both translation and administration of the scales. Based on cultural characteristics, a gender-balanced team was used and the interviewers were gender-matched whenever needed. Also, the research team had to work after work hours and during weekends to be able to interview male refugees, since most refugee men were at work during working hours and most days of the week. Conclusions: The research team’s experience showed that population characteristics including level of trauma, language, culture, gender, legal status, mobility, availability of publicly available data, and outreach-related barriers increased the challenges and ethical responsibilities of the researchers as well the research costs in terms of time, human resources and finance. Even in a host country with geographical, religious and cultural proximity to the refugees, profound challenges exist in conducting mental health research.