Cisgenesis is at least as safe as conventional breeding and mutation breeding

No unwanted genes for toxicity or allergy
Cisgenesis is currently applied for resistance to the devastating disease caused by Phytophthora infestans in potato. Control of this disease currently requires an unacceptably high input of fungicides. Conventional breeding for durable resistance is very time consuming and also causes unwanted introgression of genes coding for toxic compounds, such as glyco-alkaloids from wild potato plants.  Removal of these damaging traits by means of repeated backcrossing makes conventional breeding a very long process for several crops. In case of cisgenesis, only the resistance genes are inserted into the cultivars, without the unwanted genes for toxicity, or other unwanted traits. Because of this, cisgenesis is usually safer than conventional breeding or mutation breeding.

Gene flow
If cisgenic crops are cultivated in fields, pollen from these crops may spread and fertilize wild relatives in the neighbouring flora. Cisgenesis overcomes these biosafety issues because the cisgenes have been taken from wild relatives, and have already been present in the flora for a long time.  Moreover these genes may have been used already in conventional breeding. Therefore, co-existence of cisgenic crops and non-gm crops is neither an issue, as no flow of foreign genes occurs from the cisgenic crop to the non-gm crop.

Insertion site
The insertion site of the cisgene into the plant genome is unpredictable, just like in conventional induced translocation breeding. Therefore, several cisgenic plants are made, and the best performing plants selected, again, just like in conventional breeding.

Further scientific papers on safety of cisgenesis are