This is a protocol for a Cochrane Review (Intervention). The objectives are as follows:

Primary objectives

1. To determine the effectiveness of isolation for preventing transmission of HAI or colonization with HAI‐causing pathogens in the neonatal unit.

2. To determine the effectiveness of cohorting for preventing transmission of HAI or colonization with HAI‐causing pathogens in the neonatal unit.

Secondary objectives

1. To determine the effects of isolation on neonatal mortality.

2. To determine the effects of cohorting on neonatal mortality.

3. To determine perceived or documented adverse effects of isolation or cohorting infection control measures.

We will perform subgroup analyses based on: gestational age; birth weight; patient subgroups on whether colonized or infected; cluster type; infection type; setting type in low‐ versus middle‐ versus high‐income countries; type of neonatal unit; and type of HAI.