The aim of the present systematic review was to investigate the clinical outcomes after the perforation of the maxillary sinus by dental implants, or after maxillary sinus membrane perforation during sinus lift procedure. Twenty-nine publications were included. Failure rates of implants in cases where perforation of sinus floor had happened (11 studies) was generally low, and only one case of transient sinusitis was reported. The estimated failure rate of these implants was 2.1% (SE 1.0%, p = 0.035). There were 1817 implants (73 failures) placed in augmented sinuses in which the sinus membrane was perforated and 5043 implants (274 failures) placed in sinuses with no perforated membrane, from 18 studies. The odds of implant failure difference between the groups were not significant (OR 1.347, p = 0.197). log OR of implant failure between perforated and non-perforated membrane groups did not significantly change with the follow-up time (-0.004/month; p = 0.500). In conclusion, implant failure rate is generally low either for implants penetrating in the floor of the maxillary sinus or implants placed in augmented sinuses in which the sinus membrane was perforated. The prevalence of postoperative infection/sinusitis is low, and it may depend either on the dimensions of the perforation or on the anatomical predisposition.