Background: Pregnant women were excluded from clinical trials until the 1990s, but the Food and Drug Administration nowadays allows - and even encourages - responsible inclusion of pregnant women in trials with adequate safety monitoring. Still, randomized trials in pregnant women face specific enrolment challenges. Previous studies have focused on barriers to trial participation in studies that had failed to recruit sufficient participants. Our aim was to identify barriers and motivators for participation in a range of clinical trials being conducted in the Netherlands, regardless of recruitment performance. Methods: We performed a qualitative case control study in women who had been asked in 2010 to participate in one of eight clinical trials during pregnancy or shortly after giving birth. Both participants and non-participants of these clinical trials were invited for a face-to-face interview that addressed motives for participation and non-participation. We started the interview in an open fashion, asking the women for their main motive for participation or non-participation. When no new information emerged in this open part, we continued with a semi-structured interview, guided by a topic list. Transcripts of the interviews were analysed using a constant-comparative approach. Two researchers identified barriers and facilitators for participation, conjoined into main themes. Results: Of 28 women invited for the interview, 21 agreed to be interviewed (12 participants and 9 non-participants). For 5 of the 12 participants, contribution to scientific research was their main motive, while 5 had participated because the intervention seemed favorable and was not available outside the trial. Key motives for non-participation (n = 9) were a negative association or a dislike of the intervention, either because it might do harm (n = 6) or for practical reasons (n = 3). Combining the open and topic list guided interviews we constructed seven main themes that influence the pregnant women's decision to participate: external influence, research and healthcare, perception own situation, study design, intervention, information and counselling, and uncertainty. Conclusions: Among seven main themes that influence pregnant women's decision to participate, uncertainty about scientific research or the intervention was reported to be of considerable importance. Measures should be taken to habituate pregnant women more to scientific research, and further evaluation of opt-out consent deserves attention.