The aim of this study was to compare the breastfeeding outcome between those who conceived via assisted reproduction techniques (ART) and those who had spontaneous conception.This case-control study was conducted during a 2-year period between 2014 and 2016 in a tertiary healthcare center in Tehran, capital of Iran. We included a total number of 80 women with ATR conception and 81 women with spontaneous conception. The two study groups were matched regarding the age, parity and the gestational age. Those with contraindication of breastfeeding and history of psychiatric disorders were excluded. The breastfeeding outcome was measured using a structured-based interview and the results were compared between the two study groups.The exclusive breastfeeding was significantly higher in spontaneous conception (p < .001). The duration of the breastfeeding was significantly higher in those with spontaneous conception (p < .001). In the same way, the exclusive breastfeeding within the first week was significantly higher in the spontaneous conception group (p = .002). The ATR conception was associated with higher bad feeling during the breastfeeding (p < .001), higher breastfeeding dysfunction (p < .001) and higher experience with difficult breastfeeding (p < .001). The return of the work after 3 months was significantly higher in spontaneous conception (p = .004).The results of this study demonstrate that ATR conception is associated with worse breastfeeding outcome determined by lower rate of exclusive breastfeeding and higher rate of breastfeeding dysfunction and bad feeling during breastfeeding.