Purpose To compare the outcomes of ICSI and IMSI in women presenting with poor ovarian response. Methods Data of IMSI cycles performed from January 2011 to December 2013 were included in this retrospective cohort study. Patients were divided into two groups: normoresponder patients (NR group; patients with>4 oocytes retrieved) and poor-responder patients (PR group; patients with≤4 oocytes retrieved). Patients who underwent IMSI were matched with patients who underwent ICSI in the same period. The ICSI and IMSI outcomes were compared in the NR and PR groups. Results A total of 414 matched cycles were included in this study. The NR group comprised 324 cycles (164 ICSI and 160 IMSI cycles), and the PR group comprised 90 cycles (43 ICSI and 47 IMSI cycles). In the NR group, no significant differences were observed between the ICSI-and IMSI-treated couples regarding cycle outcomes. In the PR group, fertilisation rate was significantly lower in IMSI-treated couples (53.9 %± 36.7 % vs. 79.8 %±29.3 %). The proportion of cycles with embryo transfer (57.4 vs. 79.1 %) and the number of transferred embryos (1.5±0.8 vs. 1.9±0.7) were significantly lower in IMSI compared with ICSI. Implantation, pregnancy and miscarriage rates were similar when ICSI or IMSI were performed. Conclusions Our results suggest that unselected couples undergoing ICSI that present with poor ovarian response to controlled ovarian stimulation do not benefit from sperm selection under high magnification prior to ICSI.