In-clinic follow-up to assess completion of medical abortion is no longer a requirement according to World Health Organization guidance, provided adequate counselling is given. However, timely recognition of ongoing pregnancy, complications or incomplete abortion, which require treatment, is important. As part of a larger trial, this study aimed to establish whether women having a medical abortion could self-assess whether their abortion was complete using an automated, interactive questionnaire on their mobile phones. All 469 participants received standard abortion care and all returnees filled in a self-assessment on paper at clinic follow-up 2-3 weeks later. The 234 women allocated to receive the phone messages were also asked to do a mobile phone assessment at home ten days post-misoprostol. Completion of the mobile assessment was tracked by computer and all completed assessments, paper and mobile, were compared to providers' assessments at clinic follow-up. Of the 226 women able to access the mobile phone assessment, 176 (78%) completed it; 161 of them (93%) reported it was easy to do so. Neither mobile nor paper self-assessments predicted all cases needing additional treatment at follow-up. Prediction of complete procedures was good; 71% of mobile assessments and 91% of paper assessments were accurate. We conclude that an interactive questionnaire assessing completion of medical abortion on mobile phones is feasible in the South African setting; however, it should be done later than day 10 and combined with an appropriate pregnancy test to accurately detect incomplete procedures.