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Introduction: In this study, it was aimed to determine the problems encountered by Infectious Diseases and Clinical Microbiology residents during residency training in order to identify solutions to these difficulties. Materials and Methods: A survey was conducted between December 19 and 31, 2018 using a 46-item questionnaire. Participants were able to participate in the survey anonymously via the website of the Infectious Diseases and Clinical Microbiology Specialty Society of Turkey. Residents were informed via text message and e-mail to encourage participation. The survey included questions about current problems with the physical conditions, access to scientific information resources, the quality of residency education, examinations, night shifts, mobbing, rotations, and the possibility of following up special patient subgroups. Results: A total of 134 residents completed the questionnaire, 73 of whom were in university educational hospitals and 61 were in training and research hospitals operating under the Ministry of Health. Around 68% of the participants stated that they were working in unsuitable physical conditions and 33% had no access to medical information resources outside of the hospital. Ninety-four participants (61%) declared that their clinic had a regular training program which was renewed annually, but only 36% of these asserted that it was adequate for their training. When asked about the frequency of coworking with faculty members for scientific data/study production, 46% of the respondents answered once a year or less. Fifty-nine participants (44%) had seven or more night shifts per month. Thirty-six percent of the participants reported that they were subject to workplace bullying, which they said was perpetrated most frequently by faculty members (36%). Only 22 participants (16%) considered the microbiology training was adequate and 15% rated the training received during rotations as adequate. Thirty-three of the residents had performed a liver biopsy or been trained in this procedure. Fifty-five participants (46%) had never worked at a vaccine outpatient clinic. According to the trainees, the most important problem was inadequate education (28%) and 55% declared that they would not choose the same specialty if they entered the national medical specialty exam again. Conclusion: Residents describe many problems during their specialty training, such as inadequate education, excessive night shifts, increased workload, and workplace bullying. These problems should be presented more frequently with valid scientific data within the professional societies, and in light of this information, physician working groups should be formed to develop solutions.